Hi @iggyvolz, when I connect to those sites I'm still seeing CloudFlare certs so I don't actually see the nature of what was issued in Let's Encrypt (I guess we could also look on crt.sh to find it sooner).
The issuance limit is set to 100 names per cert, not 5, so I don't know of any reason that you couldn't get a dozen sites included in your Let's Encrypt certs. I believe that other organizations are getting them successfully.
The rate limits are described at