I have been using a modded FCB1010 with my Axe FX 2 with no problems. Except that the expression pedals are garbage.
I even changed all the buttons to be "clicky" standard pedal buttons, not the default mushy ones. Might put a springs on the expression pedals so they wouldn't be problematic...
The advantages FC-6 has over other midi pedalboards are:
Easy to program through the same patch editor.
Communication both ways.
Screens and custom colors.
No need for external power, and works with a single XLR cable.
In short - You pay for convenience.
Otherwise, all pedalboard are, is just a bunch of buttons you control your axe FX with and all of them work.
Scenes, expressions, bypassing blocks, controlling allowed knobs. Everything works.
With the Axe FX 3, you can even simply connect a bunch of momentary buttons directly to the "Pedal" inputs, and use them as a primitive pedalboard... For the most part, footswitches from any old amp will likely work.