Yes, the governance action is separately associated with each account. So a governance action by an account's proxy only sets the last time for the proxy, not for the accounts that proxy to that account. So accounts that proxy must renew their proxy request (or cast a 0-valued governance vote perhaps).
I agree there's a lot to explore on the topic of user-defined tokens. It's one of the reasons I haven't wanted to describe any particular implementation in detail yet: with the many new possibilities inherent in 1st and 2nd layer tokens, we've entered unchartered territory, so careful investigation is required to find the optimal solution.