Good point Philip. Words matter. 

Maybe make it more generic. “A boat taking a penalty that requires maneuvering…”  This way changes to the rules in the future don’t require another change to this rule. 

Everything is based on interpretation of the words.  I think that you take the penalty in the instant when you first display the flag.  After that instant the penalty has been taken.  Before that you are 'getting clear of other boats.  I don't see how this presents a dangerous or unexpected situation unless you are thinking perhaps of rule 15 and the penalized boat goes from ROW (prior to displaying the flag) to KC (the instant when the flag is displayed) to ROW (the next instant).

There are other types of penalties possible depending on what is written in the race documents.  For example, for foiling (WASZP, Moth) or high speed boats (49er, 29er, I14) you may want the penalty to be the match racing ones, a gybe or tack depending on the leg.  The original wording works and simplifies the changes that need to be made in the race documents.  It separates the what the penalty is and how it changes the right of way/keep clear rules.

I don't think this is a problem with the current rules.

44.3 deals with Scoring Penalties only, hence the title of the rule. No need to keep clear. Scoring Penalties are different to Penalties, see also 44.1, which specifically talks about Two-Turn, One-Turn and Scoring Penalties. Note that the respective first letters are capital letters, indicating that the words go together as nouns, "scoring" is not an adjective here.
Imho the rules are quite clear in this respect.

I disagree with Lorenz a bit.  'Scoring', 'One-Turn', and 'Two-Turn' describe specific types of penalties and, therefore, are adjectives when talking about penalties in general.  There is a fourth type of penalty, retiring, as described in 44.1(b).

Rule 21.2 deals with all types of penalties.  It's just that 21.2 requires that taking the penalty occur over a period of time where a boat could have to keep clear of another.  Scoring and retiring penalties happen instantaneously so 21.2 has little application.

Just as there can be other types of penalties where 21.2 could apply, there are other types of instantaneous penalties.  For example, a time penalty is often used in long distance races.

The problem with scoring penalties is that they don't remove the infringing boat from the infringed. That allows them to continue to influence the infringed boat potentially long after the incident, even if they are subsequently required to keep clear of the infringed boat.

Certainly, a boat begins taking a scoring penalty when she begins to raise the yellow flag.

When is the penalty "taken"? When all the actions required have been satisfied. Hoisting a flag is not usually enough. There's usually a requirement to draw attention or notify someone. Taking things literally you can even make the case that the penalty is not "taken" until it's applied by the scorer.

I'd go with something along the lines of "A boat that is carrying out a penalty shall keep clear" (preface with "When racing" and add "of other boats" to taste)

Bear in mind, Ric, RRS 43.1.b: 
"if the boat..., despite taking a penalty, gained a significant advantage in the race or series by her breach her penalty shall be to retire."
Maintaining a position she was not entitled to achieve could count as a significant advantage.

I'm not convinced adding more words to 21 will improve the readability of the rules. But if there's really a problem could one follow Ric Morris' logic that a scoring penalty is only taken when the scorer makes the calculation, and change 44.3 to "A boat accepts a Scoring Penalty by displaying a yellow flag."? 

Lorenz's position nicely suggests that the re-worded requirements of 21.2 should be incorporated instead into 44.2, thus limiting its force to turns penalties.

In the OP we have the answer to the OP.  44.3(a) tells us exactly when a boat takes a scoring penalty, when she displays the yellow flag.  That's the start and end to the 'taking' of that type of penalty.

To argue that it isn't until the scorer types in the penalty into a scoring program is somewhat absurd.  Following that logic a boat isn't given some of the letter scores until the scorer writes it down i.e. you haven't retired from the race or you aren't ZFP until the scorer scores you that way.

I'm still interested in some examples of the 'dangerous, unexpected situations' that might arise.

This seems to be a lot angels dancing on the head of a pin.

John, if I'm understanding correctly, as long as a boat is displaying a yellow flag, they have no rights? 

Also, what happens if two boats that are flying yellow flags (and therefore each have no rights) meet on the course, e.g., a port/starboard crossing, room at obstruction, or room at the mark... how to resolve those situations?

Al, no, I don't think you are understanding correctly  A boat is only required to keep clear of a boat that is not taking a penalty while they are taking a penalty per 21.2.  The very brief moment in time between starting to display the flag (btw, this is not getting the flag and all that goes with that) and it is actually being displayed is the time in which the boat is 'taking' the penalty.  This is what 44.3(a) clearly tells us, the boat takes a penalty by displaying the flag.  Once the flag has been displayed, the penalty has been taken, you can't undo that, and you are no longer required by 21.2 to keep clear of boats not taking a penalty.  44.3(b) then add further requirements, keep the flag flying, notifying the RC, etc. but none of that changes whether the penalty has been taken.

If you really wanted to get microscopic on this, as I pointed out previously, a boat could go from ROW to KC (just for an instant) and back to ROW with rule 15 applying briefly as they go from starting to display the flag to having it displayed.  But all this is over so brief a period of time to be a really silly distinction.

And before someone starts to argue that the display of the flag starts earlier, apply this definition to when the start of a protest flag or signal flag is considered as being displayed.  It isn't the moment you start to go below to get the protest flag or while the signal flag is being hoisted.

> But all this is over so brief a period of time to be a really silly distinction
While we are pin dancing does acquiring right of way come into it if our boat becomes keep clear as the flag is hoisted and immediately regains ROW (if she were before). I always had the impression that the whole point of scoring penalties was that they were applied after the race. Imagining an instantaneous change of ROW on the water seems to add unnecessary confusion and complication. 

If we assume that taking a penalty actually takes a finite amount of time as opposed to happening in an infinitesimally short amount of time then this is what you get from applying the rules as time goes by.  When the boat goes from ROW to KC, because it is due to her actions alone, the boats that suddenly became ROW w.r.t her are not limited by rule 15.  When the boat goes from KC to ROW, it is due to her completing her penalty and not the actions of another boat, so the boats that suddenly became KC w.r.t her are given rule 15 room.  The reality is that all this happens so fast there really is no change to the ROW/KC relationship between the boats and this is really just academic hair-splitting.

I would say that the scoring penalty is taken during the race (think also about a ZFP) but the magnitude of the penalty is not found until the race is scored and you can apply 44.3(c) .