I kind of think, that was partly overacting in terms of "this stuff is connected with this". For example, the whole "Simpsons/X-Files" thing noted in the episode, that was more of a reference or joke than an actual crossover. Hence, they don't have to be set "in the same universe" and X-Files might be not part of that long chain of flowcharts from reaching "Simpsons". Same with a lot of other things, too, I assume.
And if we kick out the reference/jokes as connections and go only with the actual crossover/spin-off, then the whole thing probably shrinks down from the 300 series to probably about a dozand or two...
I could even go further and say that cameos can also be taken out when not acknoledged within the show the character originated from as that could then just be one something that guy quickly thought up in terms of "I like that shows character I saw recently on TV, why not let it appear there in my mind as well?".
So, depending on how tolerant you are, that whole "300 and counting connected shows" isn't true. I exclude references and jokes from such an idea myself, to be honest.
Final line: Mind not blown. Sorry.