It's not a problem to mix and match types in scanlists. If you do a location based import on a Whistler scanner, everything that matches various types of activity (Fire Dispatch, Law Talk, etc.) - regardless of trunked or conventional - ends up in a specific scanlist. If it were a problem, they wouldn't do that.
Behind the scenes, the scanner is just taking everthing that was presented to you in these human manageable and readable "groups" (scanlists) and running with it. Ultimately, if you put everything in a single scanlist vs. spreading it over dozens of scanlists, the result inside the scanner is likely exactly the same.
Having said that - in a pinch/hurry - I've created scanlists that do this type mix/match programming. However, in the long run, I prefer to keep things as "separate as possible" in different scanlists to have maximum control of what is being scanned.