Hi, congratulations on the great setup!
We have two GLM 7.1 rooms. One has an older 7200 series sub with multi-channel AES/EBU ins and outs. The other has a 7300 series sub, with analogue i/o.
If you want to make use of the Genelec bass management, you need to go through the sub, and in my opinion it's totally fine to run analog line level balanced XLR's. It's all set up in the GLM software after the calibration, including the crossover frequencies. To do this in AES/EBU, you'd need the 9301A.
I'm not familiar with the MTRX, but I guess if you have the SPQ option, you could do the bass management there and just go AES/EBU straight to the monitors, no need for the 9301A in that case.
Note that in the GLM software you have to globally select analog or AES input for the whole group, no way to mix and match different formats.
Genelec have a forum with their own engineers participating, so you might get more detailed and informed answers there:
https://community.genelec.com/en/forum#/