I thought my hints were already good enough, but here's some more hints then.
Option1: Edit default skin skin1o.tgb with some bitmap editor capable of editing alpha channel like GIMP and then empty alpha channel there without completely removing it. That alpha channel is clearly for another plane so nothing useful there and it should be empty unless you like those fuselage holes. For GIMP skin1o.tgb should first be renamed to something with .tga for proper opening and then saved without RLE compression as 4 MB file before renaming back to skin1o.tgb.
Option2: Use find and replace tool for multiple files like available in Notepad++ to replace Gloss2D2o with Gloss1D2o in all .msh files of the plane. In Notepad++ this is easy with find in files tool by using *.msh* file filter in 3DO\Plane\Bombay folder. This should disable use of alpha channel in all damaged parts with original buggy default skin.
Both options should work fine and take a lot less time than writing this message, but hopefully someone learns something useful from my message. Not sure which option is better because editing one file is enough in first but second gives smaller patch and is easier really when you know how to use that tool. Anyway, both options fix bugs in original files, so doing both fixes might be the best option to avoid future issues although either option alone should already visually fix the issue.