Yes this is possible. It isn't easy and requires time and concentration
I have two different scanners and am using several different profiles. Which profile I use depends on which scanner and whether I'm travelling.
You can choose whether to download a Favorites List depeding upon the profile you wish, quite easily. However the trickier part is where you want to customize a Favorites List, as in different quick keys, systems and for a given profile.
What I've done when I want Favorites List "A" to behave differently in Profile "1" as compared to Profile "2" is this: Customize the Favorites List for Profile 1, then write it to an SD card. Then I'll "re-customize" it for Profile 2 and write it to a different SD card.
Instead of writing to different SD cards you could create some different folders on your computer. Then by changing the Sentinel Folder you can save these on the computer. Tools>Options.
The quicker option and definitely less confusing, is to bite the bullet and just create several Favorites Lists each set up as desired. Then depending upon which scanner, you can choose to download them via the different profiles.