Not sure if I already mentioned this or not but I can think of one modification that will simplify your interface board somewhat but might require some re-engineering of the board.
I think you should add a 2 row 32 pin header prior to the ODBII connection. This header should be setup so that it is pins sticking up but could be used to mount a ribbon cable to or just put jumper blocks on.
Basically you would take the lines currently going to the ODBII port and break them putting this header at the break in a manner that if one was to put standard jumpers across the pins it would connect the two sides of the break and would be the same as having the under dash version.
The point of this is then you can get rid of the under hood version and just have this one version. The header then could be used to pass the lines out of the unit as a ribbon cable if needed but the ODBII port would still be there too.
This configuration would also allow one to connect a second ODBII port to the header and by changing some wiring you could use it to go between a scantool and the ODBII port. Or lots of flexibility one doesn't have with the standard under dash setup.
And setting it up this way would do away needing two different versions.