I'm assuming a recalc is currently done using the exact times that each action (vote, accept, or bounty) took place. Almost all discussion about the recalc revolves around the fear of losing rep from deleted questions.
Would it be fair to first tally the points earned from upvotes/downvotes until the 200 cap is reached for a given day, and then apply the accepted answer and bounty points?
There is a difference between a reputation update and a recalculation. An update is done when an action is performed that affects your score. Presumably there is a current score value associated with your user record and it is simply updated. A recalculation completely recalculates your entire score based on the current, undeleted actions that affect your score.
What you seem to be talking about is the normal scoring algorithm, not the recalculation process. I don't see any real reason to adjust the scoring algorithm, but I would like to see more frequent recalculations so that the current score doesn't drift far from the actual score based on undeleted questions/answers.
I think the rep recalc should work identically to normal reputation system. If it doesn't, then using it would seem like a way of 'gaming the system'. You shouldn't have different stacking rules applied simply because a recalculation was done on your account. Perhaps that's the key right there, it's a recalculation not a calculation, it double checks your rep to find errors (from deleted posts & questions), it doesn't apply a different ruleset when calculating your total. Sure, the rep system isn't perfect, but it should at least be consistently flawed.
I think this was discussed back on the uservoice site; IIRC the ultimate decision was "works well enough as is"
