I went through a huge saga on this. I have both BMA and GRT EFIS systems. Both produce encoder output. My local avionics guy, who has a stellar reputation, but little experimental experience, said he would not wire up the avionics for me unless I bought a TSO encoder. Going ot another shop was not really an option for me.
We went around and around on it for months, also getting opinions on it from EAA and local FSDO. EAA said OK, FSDO said no. I also started what was quite a long thread about it on the BMA discussion group. In the end, I gave up arguing about it and bought a Sandia encoder, although it irked me to do so.
I understand there are lots of people out there flying IFR using the encoder from their experimental GRT or BMA EFIS. So, it really comes down to what you are comfortable with, and what your avionics installer/tester is comfortable with.
Details starting at
http://brian76.mystarband.net/avionicsAug04.htm#aug31
good luck with it - it's a very confusing and ambiguous situation
brian