Weird folder setup in Big Sur compared to Mojave. Lots of questions
Everything is correct.  This is all due to the split of the system volume (Macintosh HD or whatever you called it) into a read-only volume and a read-write volume.
Start by looking at the disk with Disk Utility.  Press Command-2 (or tick Menu -&gt; View -&gt; Show All Devices).  You should see something like this (the names will be different):

Within the APFS container you can see two volumes.  In myself case BethSSD and BethSSD - Data.  In what follows replace these with your own system volume name.
BethSSD is the read-only (highly protected) volume created by the macOS install and has the same content same on every Mac with the same version of macOS.
BethSSD - Data is a read-write volume and contains everything not part of the read-only volume. As well as your files, it includes all the application you have installed.
So we have two volumes and both will have applications - so Finder does some trickery to show them as one.
Taking your three locations (but in a different order) and a fourth:
2 The applications on the read-only volume are the Apple macOS applications and can be seen in /System/Applications.
4 (what you have not seen): In Terminal do ls /System/Volumes/Data/Applications. Here you will see all the applications you have installed - but none of the inbuilt macOS apps.
1 and 3. macOS combines the two locations above into one using &quot;firmlinks&quot;. These are what you are seeing as/System/Volumes/&lt;name&gt;/Applications as well as /Applications.
I hope that helps.  To go much further requires much mind bending!