We adjust the score as the game progresses, because you need to know who the lowest-scorer is each round.
It's pretty easy to tally up your score at any time, so I don't think it really matters, but I prefer to adjust the score whenever it changes.
I agree. The game provides a scoreboard, so you may as well use it to keep as accurate and current a score as possible.
As for the expansions that allow you to do things like discarding penalty tokens, it seems simple enough to add those points back on as you discard the tokens.