I believe that changes in the file will require unpacking it and then packing it back (for example, for * .MDT files). This is the reason for the difficulties in changing the data.
Do you have a save file so I can look at the place you mentioned? And a screenshot would also come in handy.
So with the Save Point I've been playing with it and I've tried a few different things. The save point is actually half solid and half mesh. The back portion is solid and the front portion is mesh as you can see below:
And as a result you actually can't see anything behind it:
Now if I make the whole thing half transparent, you get this:
While you can see sprites behind it now, you still can't see VDP2 stuff, and the overdraw issue leaves artifacts in the transparency. The other option is to make the whole thing a mesh that gives this look:
Which if we simulate composite blurring you get something kind of like this:
The last one I think honestly looks the best if you want the thing to look transparent, however I'm not sure if it's a change I can actually put into the game. I've yet to trace it back to the actual game data. I can find where the values are in HWRAM and I can trace the first command that starts with 0x68 to 0x0602919C which is a value of 0x0340. This get's shifted right 3 times to give 0x68. However I can't find where this 0x0340 value comes from. I've traced it to a point 0x68 is in r7 and then gets shifted to 0x0340 and get's written to that address, but I can't find where r7 is being set to trace it back from there. If where this info is in the MDT file can be found I can probably start looking for common patterns in the files with save points to implement this. But I'm not sure how easy that will be to find.
The same will most likely be true for other things that were mentioned like the stuff in Gumbo.