It is generally considered better.
The issue is a microwave cooks the coffee.
Adding heat in general is considered bad in the coffee world, like reheating any other food, really, but adding heat to maintain temperature is actually fine.
The issue coffee people take with hotplates and the like is that it doesn't heat evenly, it cooks the bottom layer. Something that adds heat evenly and gently is fine.
Although I just pour my fresh coffee into a thermos, because a good thermos will keep it at least warm all day.
Fulgora is a good place for quality. I dunno if you're avoiding spoilers so I won't go into why unless you ask, but it's a great fit.
I just got to aquilo, myself, and my current quality strategy is to stick quality modules in miners and early production, hoard quality things in many many chests, then if I want to actually make something quality, I see what I have.