I really thing you are too worried about CVs (and how many CVs there are in some specific decoder)., CVs are just registers that retains configuration settings. In the days of simple non-sound decoders it was easy to figure out the desired values on paper, then just program (about half a dozen) manually on your DCC programming track, manually, using the throttle keypad. Early sound decoders (and even some simpler current decoders, like Digitrax) added several additional CV regsters inside the decoders, but it is still easy to figure out their values and program the decoder manually.
Nowadays, there are several very complex sound decoders available, with hundreds of CV registers inside them. But that does not mean that you have to become expert and understand what they are all for. Even expert DCC users (and most of us average DCC users) don't ever touch probably 95% of the CV registers inside the QSI decoder. I don't. But it is nice to know that if we really want to futz around with some very advanced settings, the decoder is capable of such task.
As far as JMRI and DecoderPro being a crutch, nothing can be further from that! It is a very useful tool that simplifies programing of any decoder, and especially those complex decoders like QSI. Things like double indexed CV registers and setting individual bits of CVs make my brain swell, just like you feel. DecoderPro takes care of all the mumbo-jumbo for you, so all you need to worry is what you want the decoder to do. You should not feel that DecoderPro dumbs you down. It is a very useful tool that should make you forget about those pesky CV registers.
As for configuring functions for being latching or non-latching, that is not done on the decoder. It is a function of the DCC throttle and/or command station. By default, F1 (bell) should be latching, and F2 (whistle.horn) should be non-latching. If they are not, don't blame the decoder - you need to figure out how to reset your DCC throttle back to default settings. What throttle are you using where F2 is latching and F1 is not? If you can't figure out how to set it back to factory defaults, you might want to join a group for that brand of DCC system, and ask for help there.