One would hope they're also increasing rate limits along with this, but there's no indication of that yet.
> Up to 50 certificates can be issued per registered domain (or IPv4 address, or IPv6 /64 range) every 7 days. This is a global limit, and all new order requests, regardless of which account submits them, count towards this limit.
This is hard to deal with when you have a large number of subdomains and you'd rather (as per their recommendations) not issue SAN certificates with multiple subdomains on them.