Normally, the registration process uses the theme’s registration form from the frontend-app-authn URL: https://apps.lms.domain.com/authn/register. However, after signing in with SAML SSO for the first time, the registration form redirects to https://lms.domain.com/register. Is it possible to make it use frontend-app-authn as well?
It’s a bug! I’ve created a PR to fix it, it’s still waiting for approval. Anyway, will probably not be upstream before Teak. I suggest you fork edx-platform and apply the fix to your version, which is very simple.