I do use Addon Linker... but it's separate folder from where the FSDT "addon manager" is installed.
Just be sure you DO NOT manage our addons with the Addon Linker, it's completely useless because they are already using Symbolic links, and it can cause problems.
If you check the new Universal Installer which can now ran in "Installer mode" ( the "FSDT Installer" icon on the Desktop ), it has all the features you might need from an external manager, including the ability to temporarily Unlink and Relink a scenery, for example if you think it's best to do that before an MSFS update.
When I try running the couatl2.exe updater it errors out and says "PROBLEM, settings file D:\Addon Manager\couatl\Chicago Ohare V2 for MSFS 1.0.lw.xml not found, license cannot be verified.
This is not normal, that file is BOTH installed with the MSFS O'Hare installer and, if there's an update or even if you remove it by mistake, it will be downloaded automatically. This seems a problem caused by your firewall/antivirus blocking the updater.
I also tried moving the folder from Addon Manager to my custom folder and using Addon Linker to enable it with the rest of my scenery addons.
This would be a disaster. You should NEVER move things manually! There are registry keys related to the installation folder, and if you just "move", nothing will work anymore. Don't do that, don't move things, don't use 3rd party managers, use ONLY the FSDT installation programs and ONLY Uninstall using the proper FSDT Uninstaller.
Then installed again but this time I downloaded a file called FSDT_Universal_Installer.exe from your main web page.
Yes, that's the way to install anything in MSFS from now on. Is still not normal you missed that O'Hare XML file before, since it came with the O'Hare installer and not just that: the Universal Installer downloads exactly the *same* files from the *same* server. In fact, it's the *same* .EXE, just with an updated interface and, you already had it.
The only explanation I have for this strange behavior, is your firewall/antivirus blocked some files from the original O'Hare installation (that's why you missed the XML file), but it didn't block the Universal Installer *installation* for some reason, which restored the missing file, so now you can update normally.