I figured since i was doing an almalgam universe anyway I can play with the tech levels. I loathe the notion that you can just transport something by detecting their life signs from the ship (so don't get me started on long-distance beaming in nuTrek). I much prefer that you need a localised quantum scanning device (communicator or belt monitor) so the best you can do is beam down a communicator to the site of your life signs - risky since you can't be sure who or what you have detected until your local scanning device is onsite (class M planets are full of life signs) but at least with a communicator you can try and establish dialogue and beam the ting back if no dice.
As far as transporters go, I thought it makes more 'sense' if your data is quantum linked with the matter stream and then phased/exchanged with the energy of the matter stream so the person is not disassembled in a literal sense. The confinement beams' job is then to stop the quantum-linked energy leaking away so that the person reverts back in the right order at target site. If the links get scrambled you get a TMP style mess back. Boosting your matter gain is adding in replicated material based on the quantum scan you took at the start point replacing stuff that has leaked away but if too much has leaked you just get a replicated corpse.
This places more interesting limitations on transporting. If you transport too frequently you end up with cell damage (as more of your cells have to be replicated each time). Emergency transporters have lower standards on the basis that it's better to be alive with cell damage than dead