I read somewhere a long, long time ago that the sculptor of the 1/72 Yamato toys didn’t really care about the line art, or Macross in general. It was a job, not a passion project.
As for incorporating the nacelles into the leg transformation, I don’t think that would be acceptable because that wouldn’t follow the lineart at all. The only engine bits are in the intakes, for the “pre-compressor” fan, and in the nacelle bulges which house the actual engines, and those incorporate into the backpack, not the legs. If any part of them did go into the legs, you wouldn’t have a delimiter mode.
Perhaps the thing to do would be to have the wings fold flat, if they can, and make modifications to the backpack hinges to allow it to fit more closely to the actual battroid body. Or modify the wing hinges so any impediment they have to fold flat will be eliminated.