The difference is that Universal and the 6 Flags parks have much more extreme rides than WDW has. They have a lot more extreme motion, a much larger number of attractions are for the more 'adventurous' and a lot more have hanging legs with restraints that are chest/trunk restraints.
The only WDW attraction I know of with inversions (turning you upside down) at WDW is Rock N Roller coaster - and that has one inversion compared to non-Disney parks with many.
Also, the only WDW ride where your feet dangle is Soarin' - a very gently moving ride.
Disney does not give any specific warnings for people with prosthetic limbs for their theme park attractions. The only one that might be an issue at all would be Soarin'
They would not say you can't ride, but depending on how tightly attached the prosthetic limb is, you might want to remove it.
There are done warnings for water park attractions, so you would want to check that if you are planning to go to a water park.