If an alternate account earns 200 reputation and gets the association bonus, then the alternate account is merged with a different account that also has earned the association bonus, do both bonuses count after the merge?
Merging doesn't work the way you are thinking it does.
As part of the merge, everything is combined together. All the posts end up on a single profile, and your network account only has a single "HasAssociationBonus" flag attached to it. It's simply not possible to have multiple association bonuses flagged to an account.
We do not simply combine reputation values together as part of a merge. There are too many factors that can occur from a merge. In particular, up- and down- votes that would now be cast to yourself are hard deleted from the database. As well, accepts to yourself would no longer contribute reputation. Things that happened on the same day may now cause reputation caps. And so on.
Instead, once everything is transferred to the new account, we run a full reputation recalculation across the account. It will completely redo your reputation history as if everything had always been on the one account and correct any discrepancies. The process can only ever trigger a single association bonus award for the account based on that one flag being on your account, so no, you would never achieve multiple bonuses.