That's really sad! That's the first thing I found soundfont cant handle! In most keyboards, the user can always set a split function to split its keyboard in specific areas/regions so the user can attach specific sounds to each area. In all the keyboards that use the split function, the split occurs in very specific physical keys (not in the tone), no matter what transpose the user sets in the keyboard.
I thought this was a pretty basic thing, but unfortunatelly the soundfont "protocol" does not allow that (I am not blaming Polyphone, as it looks like is a problem with the sounfont/MIDI inner workings).
If I am saying something stupid or if there is a workaround/hack, I will be glad to learn