HGSS trees use multiple polygons, one for each different texture. One texture is the root, another is the main body of the tree and the last one is the side. Developers probably forgot to add the last one to that tree, so that's why you see it like that.
You said maps didn't use tiles, so that should mean each tree is its own 3D model, right? If so, how is part of it missing? (I think it might be because there are two types of trees -- ones with the little sides, and ones without.) Kinda curious, though.
I do many edits in the Diamond scripts, but I also keep the original ones in most parts of the game because the hack is an improved Diamond version, not a brand-new game. Thanks for offering for help, if there's something I need help with I'll tell you.
For now I only need to find 10 free flags (not used by any script). Do you think you can do it?