Yes, this was an incremental upgrade from 12.3 to 12.3.1. I've done each upgrade within a few days of its release. My initial move into MacOS was via this MacBook Air M1 which was delivered (November of 2021) with 11.something; upgrade to 12.something was done during setup before using it.
Re access rights. While I understand why it might be a bad idea (I installed and administered a small NetWare 2.15 network for fun back in the late 1980s), I am the only user and believe I have admin rights; I MISuse my Windows XP, 7, and 10 systems in the same way. I still in this day and age know more about CP/M and 8080/8085 assembly than MacOS, CERTAINLY more than about M1 assembly (nothing).
Re where things are, I've installed no OS helper apps. When I select Finder either by its tray icon or clicking on a blank spot on the desktop, I have top menu options including GO. Hovering over Go gives Applications which is WHAT I THOUGHT was my Applications folder. Yes, they were/are still there. They are also in Launchpad, but I use the "Go" menu for applications because they are alphabetized there by the OS.
VNC client makes a little sense; it is not in the APP store. Apple has competition, but the Windows system to which I attach to control has dual 1920p monitors which are far better rendered vy the Server's own client than by the other apps I tried.
THANKS. I'm a little long-winded, but the more I tell the less you have to wonder.
George