I have done this with a few MS installs, and all of my LS installs. Works great. Just switch the low side of the cooling fan relay via one of the outputs on the MS. Assign a programmable output with a hysteresis of 10deg so it does not flutter the relay. I also like to give a condition of RPM so the fans do not turn on when the engine is off.
I found some outputs on the MS claim they support high or low switching but can be problematic when using high. So imo it is best practice to implement low (ground) switching for all of the MS outputs.
Also, in reply to your comment about cleaning up the fuse/relay compartment this is what I did. I have about twice the fuses and relays as stock but in the same space and much neater. It was not an easy or inexpensive project though. It uses the Littlefuse POWR BLOK system. https://www.littelfuse.com/industrie...tribution.aspx