As the title really. Can you run avids with shimano? Or any disc with any brake? What the the disadvantages? Looking to run some avid discs with new shimano slx

yes you can

As long as the braking surfaces are the same size there shouldn’t be a problem. I run Avid G2 203mm rotors with my Hope mono M4 brakes witout issues.

I run Magura discs with Shimano brakes, for the simple reason that I prefer the look of the wavy Maguras rather than the boring circular Shimanos

Fairly. Some floaters are pretty bulky, so frinstance my Hopes didn’t work with my old Shimano brakes unless they were perfectly centred. And braking surfaces do seem to vary a bit though I’ve never worked out a hard and fast rule for that- Formula seem fairly narrow, Shimano pretty wide.

Most aftermarket rotors don’t come in different sizes(width) do they? So must be much the same

I’ ve run shimano, Tektro, Hayes, Hope and Ashima rotors in a random mix of Hayes, Hope and shimano calipers without issue. I have never tried floating rotors but for fixed I have yet to experience any problems other than swapping part worn rotors from a shallow pad (eg M4) to a deeper pad that contacts the rotor further in towards the hub (eg Deore).