You also have the option of consolidating multiple domain names on a single certificate. You mentioned privately that you do not want customers to be able to see each other’s domain names, but I think between Google and the CT logs, that’s not really an achievable goal.
However, if it is still very important to you to keep each subdomain on its own certificate, you can consolidate your renewals to happen all on the same day every 60 days.
There’s some discussion of this issue on Hitting rate limit after renewing certs. I’ll take your feedback as an additional request to change the exemption so you don’t need to clump up renewals. But in the meantime I’d suggest following one of the above procedures. Your use case is not a fit for a rate limit override because you can issue the necessary certificates under the current limits, given some time.