Scope creep is the whole problem. Four small extra requests, none worth arguing about, together account for the difference between a profitable account and one that quietly funds itself out of the team's evenings.
Hours per project are the only honest measure. A client with a healthy fee and three rounds of revisions on every asset can be worth less than a smaller one that signs things off, and nothing but recorded time reveals it.
Third-party costs pass through the agency: print, media, photography, licensing. Recorded against the job with the agreed treatment, they are recovered; noted in an inbox, they are absorbed.
Retainers need a visible balance. A client who can see two thirds of the monthly allocation used by the middle of the month has a different conversation from one who discovers it in an invoice.