I ran into the same issue. After doing some code-investigation i realised that i have to activate the desired CustomMicroflows in the “Provisioning-Tab”:
And do not forget to [Save] ;) and restart your server, because this takes only effekt at startup!
Maybe this is mentioned in the documentation meanwhile – i did not check that ...
It is documented :)
https://docs.mendix.com/appstore/modules/saml (3.2.3 User Provisioning):