I feel it's because Lower Deck doesn't take itself all that seriously as the other current live action Trek series, is why we like it so much; It's probably given them more freedom to play with, explore, and lampoon this entire Trek universe. But it isn't like your Family Guy and Rick and Morty, because even though it's animated, it's still a part of the Star Trek universe, and has to operate according to the rules of the universe
The only sort of live action comedy that I could compare it with, is perhaps Brooklyn Nine-Nine. The precinct is filled with these goofball quirky cops who all have their issues. But when the time comes for them to be "serious," cops they step up.
Or even going further back to shows like Sledge Hammer! or Get Smart. They were comedy shows, with action elements, and if you want to pull something like that off, you can't downplay the danger. That way it really hits home when they don't pull their punches like having the Pakleds destroy the Solvang.
To me, Lower Decks came about because Mike McMahan took all those things we as trek fans love to joke about that are funny to us, and built a show around that.