This depends on the situation. There is at least one I run into all the time that does interfere and which makes using a preset a must.
The exposure module, using the scene referred workflow, does not take an image shot in M mode into account. It blindly applies any exposure compensation it finds. When shooting in manual mode this should not be the case.
I’ve mentioned this before: Compensate for exposure correction - #3 by Jade_NL
This intelligence might not be that easy to implement, though.
BTW: I do not think that needing to use a preset is a problem in this case, even though it would be nice if darktable would pick this up in the first place.