I don't know what plans you are looking at, but the Air Trails plan (Old Time legal 1951 version) did have wheel pants.
As to the difference between this and the Ambroid kit, the kit was based on a later version of the Stuka (trying to be up to date at the time. Today we want to revert to the earlier version) and there were more differences besides the flap shape and construction. Check the cowl shape and location, for instance. And the canopy. There are minor "tweaks" here and there which would not make it old time legal even if you changed flaps (and are honest).
Yes, with all the flap about honesty in that other controversy, honesty is something we live by. You enter an Old Time plane and you tell the director you followed the plans. You enter a classic design and you mention that you did or did not make modifications. Unless something is obviouisly wrong, people accept our honesty. (Who brings a ruler to check to see if you increased the moments by half an inch or the size of the elevator just "slightly"?) Even in the PA events, sometimes they will check our lines. Usually they don't. We tell them what engine is under the hood for the pull test. How often have they checked? And for the weigh-in at the FAI, is it possible to take out the tip weight, the tank, and other "non essential" portions of the plane before weigh in?
Honesty is always a part of our event, and we rely on that honesty. In your case, the answer is "no" to its being legal for OT stunt, even with a change in flaps.