I'm not quite sure how your base domain would affect, but from the rate limit determination of *.apps.mydomain.com, each of the subdomains are considered as a "new domain" for rate limit purpose. (So you can imagine your apps.mydomain.com would effectively become something similar to a domain extension)
There is something you need to keep in mind, though: you won't be able to get a certificate for apps.mydomain.com -- it would be just like asking for a certificate for .com. I don't know how this applies to mydomain.com.
So you should probably register a second domain myuserapps.com and put that one in the PSL.
@9peppe Thank you for your replies here, they helped me also. I just wanted to point out that according to this Wildcard certificates and Public Suffix List you can issue a LE certificate for a domain that’s in the private section of the Public Suffix List, just not for one in the ICANN section (.com, .org, etc.). So, unless something has changed since @jsha’s reply in that post, @jacky.jones should be able to get a certificate for apps.mydomain.com.