The keys required to sign certificates and OCSP responses are stored on a Hardware Security Module. The signing operation takes place on this device (the keys are not allowed to leave it at all). These things are very expensive and only support a finite amount of signing operations per second, hence the rate limit.
Here's a post confirming this for your reference (there are probably more detailed ones somewhere else, it was the first one I found):
Exempt FreeDNS domains from the rate limit - #23 by jsha
Again, I agree that there are valid use-cases where you just can't solve a problem with the current rate-limits in place. I'm sure Let's Encrypt would love to provide a solution for that as well. It's just not as simple as "throw away the rate limits". The new solution would have to scale while not degrading the service level for all other users. Give it some time and I'm sure something will be worked out.