shortly after the fork Nextcloud introduced the first API break [1] for apps registering stuff at the admin backend followed by additional changes for 3rdparty apps in [2] and now your mentioned third problem in [3].
Something like this is causing:
Double of work for app developers if they want to keep compatibility with ownCloud and Nextcloud
App developer which can’t handle this additional effort to choose sides between oC and Nc
the need of forking apps to make them compatible with oC again
IMHO this is one thing where Nc is trying to pull users on their side by introducing such incompatibilities / API breaks which makes it impossible for oC users using apps written for Nc.
Thats one of many reasons why i dislike the Nc project and why i would never move my installation to Nc.
If they wanted to keep app compatibility between oC and Nc they could have done this. Instead a community gets splitted and misused to taking sides between both.