The 20 per week limit has been an issue for large organizations with tons of different subdomains managed by different groups. Universities are a good example: you might have things like bobsmith.faculty.example.edu, cs101.compsci.example.edu, etc., which all count against the example.edu rate limit.
This can especially be a problem because the renewal exception to the rate limit doesn't work like you might expect. If a particular cert (meaning the exact same set of domains) has already been created, it can be renewed regardless of whether it would exceed the rate limit - but it still counts against the rate limit. If 45 certs have already been renewed in the last week, you can only create 5 new ones. If 80 certs have been renewed in the last week, you can't create any new ones. They plan to change this, but it hasn't happened yet: https://github.com/letsencrypt/boulder/issues/2800
Some organizations have gotten rate limit exceptions to handle this particular issue. Maybe they looked at some internal metrics and decided raising it to 50 would reduce the number of exceptions they have to make while still curbing misuse.
Because you could have 50 subdomains, for which you'd need either a wildcard cert or 50 separate certs.
That might seem like a ton per week, but consider a PaaS (example-123.herokuapp.com) or a blog platform (example-diary.someblogapp.com).
Personally I'd prefer a wildcard cert there, but at organizations where certificate inventory is a requirement (where they need to track, procure, and invalidate on a per-subdomain basis) Let's Encrypt is a solid option.
"The main limit is Certificates per Registered Domain, (50 per week). A registered domain is, generally speaking, the part of the domain you purchased from your domain name registrar. For instance, in the name www.example.com, the registered domain is example.com. In new.blog.example.co.uk, the registered domain is example.co.uk. We use the Public Suffix List to calculate the registered domain.
If you have a lot of subdomains, you may want to combine them into a single certificate, up to a limit of 100 Names per Certificate. Combined with the above limit, that means you can issue certificates containing up to 2,000 unique subdomains per week. A certificate with multiple names is often called a SAN certificate, or sometimes a UCC certificate."
In my case, we provision a wild card for accounts on our service (*.account.companycustomers.com). While we bundle these together with a few other sign ups, it's sometimes better to get it out the door initially, and then bundle them with more subdomains on renewal. We have received an exemption to the certificate limit per domain to achieve this at least.
