Last time I checked, TPT didn't have any level of alchemy implemented, so I can't help with your transmutation problems. As for stopping black holes from forming, they form when more than 5 particles are stacked on top of one another, or 1500 when in EHOLE, a type of wall. These are hard limits, not much can be done about them, but the EHOLE trick generally solves black hole problems.
If you are using console to "stack" more than 5 particles then they will get converted into BHOL.
However there is a way to prevent this using Ehole wall. This way the particle stack limit increases from 5 to 1500.
Note that fusion and some other reactions also lead to BHOL formation.