From my experience, Health Authority submission documents generated by the CRO (e.g. CTAs, substantial amendment notification forms, cover letters, etc)
are filed in the study eTMF. CROs usually do not have access to file directly into the Sponsor regulatory system.
I have seen Sponsors file regulatory documents directly in their internal system for only those countries where they hold submission responsibility. This is common for USA FDA.
LMK Clinical Research Consulting