The iEFIS "Lite" versions output serial (RS232) altitude encoder data. They don't output the older style "Gray" (Gillham) code format. The full flavoured version outputs both.
This is only a problem if your transponder doesn't accept serial altitude data, which shouldn't be an issue with any newer/modern style transponder.
They both use the same altitude encoder as far as I know (the Lite's encoder is in the display unit, and the full variant's encoder and its Gillham output socket is located in the "iBox", which you don't get with the Lite). The whole thing about the "Lite" is just that it sacrifices certain input/output connectivity, which includes Gray code format, for a much more compact system. It uses the same software & hardware - connectivity aside.
Just had a "Lite" installed in my Pitts connected to my Trig TT22 transponder. No issues as far as I'm aware.