Brad -
At the moment I can't say that I have found an entirely satisfactory solution.
Decoders without back-EMF, such as the NCE D408SR (my standard decoder), did not achieve satisfactory smooth starts in my C&LS engines. That appeared to be caused by the locomotive's unusual gear ratio. The locomotive would not move without opening the throttle quite far, but by then the throttle was already set for surprisingly fast running. So a good start required "blipping" the throttle to try to kick the locomotive free. Current 408 decoders have optional low-speed kick pulses much like the venerable TAT-4 DC throttle but even these were not quite up to the task. This said, I plan to continue using the 408 in my non-C&LS locomotives as I am otherwise quite satisfied. It is a robust and thin design with a built-in heat sink, and easy to fit in most locomotives.
These days I would choose a decoder with back-EMF as it can regulate speed much more quickly and precisely than we can. A second factor might be sound.
The NCE web site shows a D408E-SR back-EMF decoder, but after many, many years it is still "not available."
I tried a Digitrax decoder but was never able to adjust the control CVs to get smooth running. It tended to buck and sounded like a hit-or-miss gas engine. I was also curious why the decoders defaults turn off back-EMF. Perhaps I discovered one reason. Perhaps others will be more successful in tuning the CVs. I gave up.
The Lenz back-EMF decoders I've operated in other locomotives always provided outstanding low-speed operation. However, in my HO days I had troubles consisting Lenz decoders with back-EMF turned on. The speed regulation was so precise that two otherwise identical locomotives would fight each other for dominance. I can't say if that would be an issue with their latest O-scale offering or not. We never consisted two Lenz-equipped locomotives on David's old layout. Lenz decoders also tend to be taller, but the green screw terminals could be unsoldered if need-be.
I'm personally not a fan of QSI prime mover sounds so I have no real experience with them. I did watch a friend's Atlas F-unit start run very smoothly on DC despite the notorious twin-motor "china drive." Nor can I say if there is room to fit the decoders.
Some folks have tried using HO Tsunamis in a few O-scale locomotives. I haven't measured the current draw on my C&LS engines so I can't recommend trying that unless you don't mind risking a decoder. That said, since it uses a 24 volt motor the stall current should be about half that of the usual 12 volt 8xxx Pittman (about 8 amps for the P&D 12 volt drives.) The modified Tsunami from ProtoCraft is intriguing but I haven't (yet) tried one.
I have absolutely no experience with ESU decoders. Some modelers in HO have given good reports.
Soundtraxx seems unlikely to ever produce an O-scale decoder (the company representatives appear to be annoyed whenever I ask.) I have started my own Tsunami booster design but that project has been put on the back-burner. When it comes time to paint my C&LS engines, I will probably try this first, and perhaps a ProtoCraft modified decoder.
There should be plenty of room in the long hood of the RS11 and RSD12 for at least a motor decoder. I've never seen the inside of the Trainmaster, but the long hood is quite wide. Internal space at the radiator end may be consumed with the operating fans and control board. A Tsunami 750 should easily fit in any of the short hoods.
Sorry I could not give a definitive answer. Hope this helps.