

Seems to depend on the flavour of Android. What version/brand do you have? I know my Pixel asks first unless I allow it more generally.
You may be looking for the “Instant Apps” settings though. Searching “links” in your Android settinbs should provide a similar result regardless what brand of phone you have though.
Flatpaks are basically containers, allowing applications to maintain their own dependencies separate from your system. It’s similar to a Windows program shipping with its own precompiled DLLs, helping prevent dependenct conflicts when you go to update something you installed with pacman or yay.