I read the text of the rule as saying that the relevant appendices only apply between craft of the same type and that if craft are not the same type, eg windsurfer and kiteboard, then unmodified RRS18 is in force. 

Which class says Rule 18 doesn't apply? Reading the definitions you have pasted above, I read that rule 18 applies to each of them.

For the iQ foil, Appendix B replaces the definition of 'zone' with the concept of passing the mark "Rounding or Passing A board is rounding or passing a mark from

the time her proper course is to begin to manoeuvre to round or pass

it, until the mark has been rounded or passed."

As with other mixed class racing, I would presume that the zone/passing area is reached when the inside boat reaches the edge of the widest definition between any of the 3 classes (usually governed by 'longest boat'). With the additional rule implications of the kiteboarder keeping all of their gear clear of any board clear ahead/reaching the zone(/passing area) before them - even if they are not overlapped. [App F, 18.2 (a) 2] and the Appendix F definition of keeping clear and giving room to keep clear including room to move her kite in all directions without immediately making contact.

In practice, if any of them are getting close enough that distance from the mark; whether they have reached the zone or passing area; or whether they have provided enough mark room per the other class's requirement to round AND there is uncertainty about whether enough room to round has been provided - they are probably too close. Surely any OA organising mixed racing of this kind would want safety and lack of contact to prevail? 

So this is not the scenario for any competitor to be pushing whether the edge of a zone/passing area has been reached, or whether an overlap was established. (if the kite is inside or simply there first, there is no provision for another class to 'nip inside' as she has right of way & mark room, including room to move her gear in any direction she wants....I certainly wouldn't want to be the foiler pushing my luck going inside after being clear astern & then finding a set of kite strings closing on me at 15 knots!

Is there an actual scenario of which class reached a zone/passing area first? Or is it hypothetical? In which case I can't see that your query exists, other than 'passing area' might be quite widely defined for the board depending on wind strength?

Mark it's a tricky situation, especially if you have at least any of the two classes racing on a course together. 
The introduction in the RRS clarifies that when rules of an appendix apply, they take precedence over any conflicting rules in part 1-7 and the definitions, but it is silent on the conflict of rules between appendices. 
So, we could consider the board closure to the mark to decide the size of the zone (as per its appendix) to then apply the RRS 18.