The guitarist & bassist quit after the shitshow that was Pretty.Odd. It was Ryan Ross (guitar) who wanted them to sound like The Beatles.
So for Vices & Virtues and Too Weird To Live, it’s Brendan + Spencer Smith (drums) + various cowriters and producers (including the replacement band members, but they were never full members, more employees a la Ronnie Wood when he first joined the stones).
Spencer Smith officially left before Batchelor, although by all accounts he’d been out of commission for ages due to personal problems. Then the bassist came out and said he was no longer ‘contributing creatively’, so Batchelor is all Brendan, every instrument except the brass. There’s a few Rivers Cuomo co-writes on that album too (most of the big singles IIRC)
Then during the Batchelor cycle, the guitarist got kicked out for noncing and the bassist left for other reasons, so the current lineup has only actually put out one album together.
I’ve only ever heard very nice things about Brendan Urie as a person, and I’ve a lot of time for anyone who can collaborate with Every Time I Die AND Taylor Swift, but you have to reckon on a certain level of bastardy just to survive in that business right?