I have an industrial VPN with ~300 embedded devices behind them. For some reason the user wants to access to each one of it via https.
I thus set up an Apache proxy which proxies https://device_n.vpn.cust.tld to the VPN device (and some auth)
LE cant issue 300 certificates and it would be very ugly.
For systems not explicitly public, whitelists are almost always better than blacklists.
The limit is 100, unless they removed that when I wasn't looking. Back in the beta I tried one domain, a handful and then, because I couldn't find a technical reason why SAN should be limited, I tried 500. It fails. I have many certs with up to 100 and would be happy if this changed.
(And if so, in the prior commenter's situation--okay, create three certs. LE might not support 300 certs, but 3 with 100 SANs should work just fine.)