We really have to be practical about mods. Fidelity points, etc are to prevent the extremes, not the necessary. For example, a Nobler with a foam wing would lose some fidlity points since Noblers did not have have a foam wings, but it would be allowed to fly. Extremes would be add a couple inches to a tail moment, or using a tuned pipe, or asymetrical wing panels being changed to less asymetry or equal panels.
There have been arguments about tail wheel heights, but again that would only be a small loss of fidelity points, but tail wheel heights always varied some. Some people think the Gieseke height tail wheel shouldn't be applied to other airplanes, but personally I would rather close that book.
Remember this is not a scale contest, we should enjoy it.
Designers have always played with flap width and length on their airplanes. I have seen many original airplanes over the years that have flaps trimmed, or pieces add to, and painted later when the mod worked out. Even shortend flaps, with the outboard section changed to trim taps, are not uncommon.
Widening the fuselage to accomodate an engine certainly is no problem. This has no advantage aerodynamically.
Engine improvements, to me, are also no problem. I am currently working on Jack Sheeks "Sea Vixen". Jack had engines ranging from a .35 to a .40 to a .45. in the original airplane. Some details and dimensions are simply not on the "Sea Vixen" drawing. For example, the fuselage formers are not showm. The article says they are 2 1/16" wide. The top view show the formers "close to 2 1/8" but aft of the ply doublers and about 2 1/16" between the doublers. If I made them to that dimension inside the doublers, the mounts would be to far apart for the ROJett .40. which has mounting holes that are close to edge of the mounts. I will also use 1/32" ply doublers instead of the 1/16" that were typically used. My solution will be to have the mounts the proper width for the engine and add to the width of the fuselage sides to get the proper width. I would not be concerned about adding fuselage width, but I won't decrease the width.
Likewise I wouldn't complain about changing the thrust line 1/16" to add a plate under the engine, but in most cases the mounts can be moved the thickness of the desired plate, keeping the thrust line the same, with the added avantage of giving room for tank adjustment.
Again, we like to replicate the originals as close as we can, but keep in mind the the designers made changes, and this is not a scale event. Have fun with it.