Every PC game is a little different. An approach that works for one may not work another. GTA has individual sensitivity adjustments for each controller mode (walking, driving, flying, etc). You might find something useful in there, but you are looking for a more general approach.
When the CronusMax is passing through commands on the PCPROG port, it can't do anything else. It can't run scripts (slots). X-Aim will run scripts, so you could adjust any value in there, if you were playing on a console.
When running QMP with an UltraStik and a CronusMax, the two streams of USB data are independent from each other. You can turn off the CronusMax driver in the QMP (Misc tab) and still have the UltraStik values passed through to the quadstick. Then X-Aim could take data back from the quadstick and massage it, and pass it through to the CronusMax, but for PC games, X-Aim can't be used since it has to be in front.
Right now the QMP+QS just passes the UltraStik value straight through. No scaling. There is no reason I couldn't add scaling preferences for the "external pointers". I'm adding a mouse location and button capture to QMP to support the Tobii EyeX, for console games, and since I'm going to be making changes to that part of the program anyway, I'll add some scaling preferences.
X360CE has axis scaling adjustments. For PC games that support X360CE, you can create game specific configurations and adjust things like deadzones, anti-deadzones, acceleration and sensitivity. Wouldn't need to use the CronusMax for those games.