Since the MR86 is a 4x4 antenna array (and you can’t tell it to be a 2x2) you will likely see some issues since the coverage area on two of the antennas will be different to that on the other two. That’s not to say it won’t work, you will take a performance hit as MRC is likely to not provide as good a result, you probably won’t get as many spatial streams up and running, and beam-forming won’t work as well if you’re trying to reach distance. So, in summary the throughput compared to if you were running two MA-ANT-27 on each MR will be less.
You should definitely be terminating those other ports, remembering there are two connections on each port that need termination one for the 2.4GHz radio and one for the 5GHz. Running them unterminated risks damaging the unit.