See Pinned Ubuntu Dock Apps in the Application Grid
Quoting: See Pinned Ubuntu Dock Apps in the Application Grid - OMG! Ubuntu —
Not everyone likes this behaviour, especially if Ubuntu Dock auto-hide is enabled.
Naturally, there are 3rd-party GNOME Shell extensions one can install to make sure all apps show in the main applications grid irrespective of whether they’re pinned to Ubuntu Dock (or Dash to Panel, etc).
The best known of these is Favourites in AppGrid, but there are two big issues with it.
First, Favourites in AppGrid has yet to be updated to work with GNOME 46 or 47 (though with manual config file editing it can); second, installing that extension breaks the ability to rearrange icons in Dash to Dock (which Ubuntu Dock is a fork of).
So someone has forked, renamed, and released a new version of this GNOME Shell extension (‘Keep Pinned Apps in AppGrid’). It supports the latest versions of GNOME Shell and resolves the underlying issue causing issues with dock ordering.
Or to quote the GitHub page for it (clearly aided by a GPT1): “[t]his repository aims to provide a simple yet effective fix to this issue, preserving the GNOME Dock layout while ensuring pinned apps remain visible in the grid.”