Yes, and that is stated as recommended (see below).
Yes (see account creation limits below).
When using IPv4, the limit comes out to 80 per day (probably lower than you require).
When using IPv6, the limit comes out to 4000 per day - which should be more than enough.
From (Rate Limits - Let's Encrypt): You can create a maximum of 10 Accounts per IP Address per 3 hours. You can create a maximum of 500 Accounts per IP Range within an IPv6 /48 per 3 hours. Hitting either account rate limit is very rare, and we recommend that large integrators prefer a design using one account for many customers.
You're not missing anything on the rate limits page: It's totally fine to get thousands and thousands of certificates for different domains.
Some of the rate limits are relevant, like the HTTP request per second limits, or the pending authorizations limit, and the ACMEv2 new orders per 3 hours limit.