That is exactly what I mean with “redundant”. Why do you block access to something which does not exist anyway? Could be seen as a security measure, but since you obviously have issues with your setup, at least try to undo this change.
Still not as you expect as you opened a bug report at Nextcloud. Note that this is not a Nextcloud issue but an issue with your Apache setup, so that bug report is misplaced.
How do you know that it is not the other way round, which config overwrites which/has higher priority? And again, that default config shipped with the Apache package is a template which is not used and not enabled by default, even actively disabled by Certbot, reasonably, since it doubles/conflicts with the Certbot config.
And you enabled the default SSL config. Again, everything works fine without any custom changes, but with your multiple redundant configs if does not all work as expected. So before opening bug reports please do test the untouched default config and apply your modifications one by one to find out which one breaks the expectations.