There is nothing wrong with using rootstock for bonsai, however you just have to accept that the rootstock won't have the same characteristics as the scion cultivar.
This could be bad, or not an issue, depending. Usually rootstock is chosen for favorable characteristics which often include, health, strength, and rate of growth. So you might have a JM that is a dwarf cultivar, but the rootstock is significantly stronger. It may not matter to you if the tree does what you want it to do
Note that with some tree species the rootstock may be a completely different tree
species, so you might have a completely different experience. I noticed this particularly with my citrus trees in Southern California.
As an example check out this listing for C-35 citrus rootstock. Note how they specifically call out the impact on tree size, fruit yield, and resistance to disease and pests... and the fact that it is a poncirus/citrus hybrid. So if you decided to create a citrus bonsai off your rootstock, it might not even bloom... and there is no guarantee it would fruit. And yet the same rootstock could be used to grow oranges, lemons, limes, and grapefruits(!)
Strange but true, there are trees out there with 40 different cultivars grafted on a single rootstock. A fun experiment that requires a lot of labor... but it
can be done. I had a peach tree in landscape that had three different cultivars of peaches on a single tree. It was a PITA... because one cultivar was stronger than the others and kept needing to be trimmed back in order to balance strength across the three cultivars and prevent the dominant one from taking over.