Are the confirmation bots required (can't see this in your protocol standard) to continually compare their database states with the actual state of the blockchain?
Yes, sort of. The blockchain is just a list of messages; it's not really useful to think of it having a "state." Notice that the protocol makes no mention of posting confirmations, only about validating confirmations. The pocket database is a function only of the Steem blockchain, which I believe is clear from the protocol. As such, the bot's database cannot be updated to reflect the fee until the confirmation message is discovered in a Steem block. Once it is discovered, if it is the first confirmation for the associated transaction, its owner is credited the fee. Then, any subsequent confirmation for the same transaction is invalid, because the fee has already been awarded.
A bot that posts confirmations is always running on top of a program that parses the blockchain to determine database state.