I never looked at the algorithm use to generate "uidnumber" and would not care that much until this is proven that issue you face with account limitation is due to this algorithm.
Problem, unless I misunderstand your explanations, is that your are testing in different direction which makes, at least form my side, things a bit confused.
What I would like to understand is whenever there is any limitation when you create accounts, either manually or using script.
When I say account, I mean Zentyal basic account.
If "file sharing" module is installed, this should also create accounts in the "Samba LDAP" repository.
Then "adding account" to Zentyal "domain" (Samba DC) which is in fact also having new workstation joining this domain, is another topic.