Why do some Flatpak software recognize system settings, while others do not?

Recently, I upgraded my PC to Debian 12 and chose KDE as my Desktop Environment. For this fresh installation, I decided to maintain only the core packages managed by "apt" and started using Flatpak for my apps.

Some Flatpak apps perform flawlessly out of the box, such as LibreOffice and QGIS. They adjust the language to my localization and adopt the theming from my system effortlessly. However, others like Obsidian and Zotero require manual adjustment of settings by modifying the configuration files.

I understand that Flatpak applications are sandboxed, so I initially expected them not to recognize my system configuration files. However, I am puzzled as to why some apps do recognize them while others don't. I have attempted to read some documentation on Flatpak itself, and if I understand correctly, Flatpak has the capability to read from system configuration files. However, I haven't fully grasped how it accomplishes this (is there anything to do with portals?) and why it only applies to certain packages.