If re-watching Bender's Big Score has thought me anything, it's that paradoxes are always corrected, and copies of people are always doomed.
Taking that into account with regards to Chariot Of The Dogs, when the Freelance Police did quite a lot of time travel, it would appear that in 305 we discover that Sam & Max went on two totally different routes, maybe somehow this created duplicate copies of Sam & Max, and the reason for them to turn into horrible monsters was not a mistake... maybe because THEY were the duplicates. And thus, were destined to be destroyed.
So if you think of it that way... the Sam and Max that got reunited in 305 were perhaps not the new Sam & Max, but the real Sam & Max.
..Either that, or it had something to do with an alternate universe. But I don't want to believe in that because it was time travel that was involved and not travelling to alternate universes.
You have no need to agree with this, I just wanted to share one of these theories I like to make up after I finish a game that's left quite a bit up in the air for debate. :)