Disagree. Frank was super-prolific. The problem with super-prolific people that actually show all their work is that they are not all gems. But there's great Zappa stuff from every period as far as I know. And I do find many of his lyrics funny. "Let's Make the Water Turn Black" from the 60s is great, but "I Come From Nowhere" in 1983 or whatever is even better. That is progress, which I like to see.
For an opposite perspective to yours, there's the Captain Beefheart camp. My understanding is that Captain Beefheart had the REAL sarcastic, condescending misanthropic personality, and he couldn't work with Frank anymore because Frank was such a pop-star user-friendly sellout!
You can isolate parts out from each other. But your reputation is mostly built on the entire thing you do.
I think Frank's sheer musical brilliance allows people to overlook a lot of his antics. But it's those antics that take away from what would have otherwise been considered unquestionable genius if they were absent.
I won't comment much on Beefheart. Met the man. Did not like him. At all. One of the very few people I ever met I would have gladly punched in the mouth.