Safe data of apps to different locations? [App / Feature]

Not quite sure where this belongs to but I have something thats bugging me quite a bit.
I’m pretty anal when it comes to keeping an organized file system, which isn’t a problem with NextCloud perse, but it creates one, when taking other apps into account:

I use the Carnet and Recipes app and love them so far, but they insist on saving their configs / metadata in locations of the root folder of my user account! Recipes: /Recipes, Carnet: /Documents/Carnet.

This annoys me alot, as there seems to be no settings option to direct them to another save location, and the ability to hide folders is UNIX like, aka renaming ./folder to ./.folder, meaning that the folder will be recreated visibly.

Is there really no way to change this on a general basis?
Any help would be appreciated.