You probably don’t need to take any special precautions about renewals. Your certificates are all for different domains, so they are all rate limited separately and certbot-auto renew will only renew them every 60 days anyway.
However, I think you may have misunderstood how the rate limit is applied.
You can issue as many certificates as you want for different domains. The rate limit restricts how many certificates you can have for subdomains of the same domain. So you don’t really gain anything (from a rate limiting perspective) by combining subdomains of different domains into a single certificate. (In fact, if you frequently add new subdomains to the certificate, you could even end up hitting the limits sooner!)
@jsha I suppose it’s Is it possible to use LetsEncrypt on 150+ unique subdomains only?