As of 09/12/2022, the ever so loved Trenchbroom still does not have support for Radiant or Hammer style models, color selection, transparency or groups (some of these have equivalents but not in the same way that Hammer utilizes these)
Along with all that, transferring a .MAP out of Trenchbroom and getting it running in JACK can produce several interesting issues, not the least of which is various texture alignment problems, all of TB's groups becoming func_group and slightly different interpretations of the plaintext coordinates. Don't even get me started on transferring a JACK map export over to Trenchbroom, it's a nightmare. 
JACK produces some strange context in the fields of vertex coordinates which Trenchbroom outright hates and will crash for it and the worst of all this is the disparity between texture wad location fields which requires you to re-locate all the texture wads every time you take your map into Trenchbroom from JACK.
Writing a bash or powershell script to handle this is possible but I'm very worried about indenting one line or changing the wrong fields in the plaintext of one of my maps with a script so I still do this manually.
Still, the pipeline from Trenchbroom to JACK is too powerful not to use in the long run. I love Trenchbroom as an editor and it makes mapping on a 45° actually not make me want to rip all my hair out with flex tape as is the case with Hammer/Radiant style 2D editors.
The power of creating the bare bones of the map in a swift and intuitive all 3D editor and importing it later into JACK works well when you've done it for long enough. I have gotten the feeling in the past that it's limited my creativity and forced me to brainstorm the whole time as to the purpose of the map because all the funky teleporter rooms, camera rooms and without a doubt all the entity placement must be done in JACK.
If there are any veteran mappers out there that know how to alleviate these issues I would be overjoyed to talk to you. For now though the results still come through with only occasional explosions of technical debt.
