Is’t very much possible to generate one certificate with a heck of a lot of subdomains. What is not possible, is to generate a heck of a lot of certificates with just one subdomain
Now, you’ll have to wait 7 days (or less of your first certificate was issues earlier) for the rate limit to be removed.
The problem with the suggestion to add additional sub-domains to one certificate is that when the sub-domains are on separate servers they won’t validate.
Even with careful timing of certificate requests, it is only possible to keep 64 sub-domain certificates issued or renewed within a 90 day window. Some of us have the potential need for hundreds of sub-domains running on separate servers.
BTW this issue here is also the reason why some dynamic DNS services may be problematic, but there are things the service providers can do to solve this. More information here: