How to fix custom song glitches on emlators.

So basically the instrument patch has to be scrapped for any kind of emulation accuracy, unless a workaround can be found to load two or more instrument banks separately on an as-needed basis (which would be pretty complex).

No. I did not expressed myself clearly. That limit is for each song (I edited the first post). In fact having the RS3 instruments can help in a lot of songs, since they generally take less place than their FF6 counterparts.

In the case they really don't take space...

I think this is a fast assumption, the only way to really know is to test it.