Couple things that come to mind:
If you plan on using a MMM then I don't think you can if you have a subframe backhoe.
Kubota does change something on the side of the tractor (brackets) when the 3PH backhoe is installed. They also install a heavy duty top link bracket. If you go with the Kubota 3PH backhoe you need to make sure these things are installed.
I have a Kubota 3PH backhoe on the back of my
B2910, and I personally do not feel you need to do more than the Kubota engineers did when they designed the system. I would hesitate to make any modifications, for fear that I might end up with something that stressed the tractor in some way I did not foresee. But that is just me.
That being said, it sure seems like subframe backhoes are the way to go and if there had been a subframe Kubota backhoe for my tractor I would have got one.
You could go with a Woods or other brand of backhoe, that uses a subframe if you do plan on using a MMM. I did not consider that option because it was my fear that if something went wrong and the tractor broke, when it had a non-kubota backhoe on it, I would have to suffer through a lot of finger pointing and delays in repair/warranty denials. This was simple speculation on my part.
I think the claims of tractors being broken in half by 3PH backhoes are over blown, but such things have happened. So this possibility is certainly a disadvantage to some degree.
The subframe takes away a little ground clearance from what I understand and gets in the way of an MMM and perhaps something else (don't know what though).
I think either can be very satisfactory, provided that they are installed properly, as designed for the tractor they are going on.