Here is a quick test I did on an earlier version of the model. The original plans I used were very inaccurate so I scrapped this version. As a test I smoothed the fuse and wings to 2 levels of linear subdivision and then booleaned out the landing gear panels and the fit is near perfect.

The corners are tight because I made the cutter very quickly and did not smooth any of the corners but smoothing the cutter prior to the Boolean operation will fix this. Since the end model will be smooth to this level of detail anyway I see no problem with the method although I have not considered laying out the uvs yet and what impact this will have no that process.