Go to love Microsoft. Before I start I want you to know it's not your fault but you are experiencing a very weird bug that it's rare to happen due to an oversight of Microsoft and... your mobo manufacturer. Even if you search the internet for LTSC and S mode you will see only 2 or 3 other instances of the problem. As far as my personal experience I only came across this bug once. I want to make this clear, it's not your fault or the windows modder's fault.
Let's start from the beginning. As you know, Windows S is a special version of windows that will allow the installation of apps that ONLY come from the store for security control. To make sure that this is the case, only some devices can enter in S mode and there are certain requirements. For example, you need UEFI enabled PCs, the secure boot must be on, etc.
That means your PC somehow is S enabled and should have a windows license stored in UEFI. That's why I asked if it was a brand PC like ASUS, ACER, HP, etc. Additionally, I think it asks you to log into your Microsoft account during setup which from there retrieves and enters the S mode.
Here's where the bug is. MS after 1803 builds in any windows, autodetects if the PC is S mode capable, and starts S mode automatically. MS probably forgot to put an exception for the LTSC build. So you installed an OS in S mode, that needs the MS store to get deactivated but has the store removed... brilliant. Since this affects builds after 1803 that's why you didn't have a problem with LTSB which is 1607.
Solutions:
The way I solved it was to install the original windows that came with that PC, deactivate the S mode and disable secure boot from bios. That allowed me to install LTSC normally but in your case, it didn't work (I hope you tested with a build greater than 18xx). I can think of some extra things but will be speculations and can't be done from range as it needs a LOT of feedback and that will take ages. So all I can do is give some advice and depending on your level of knowledge try them.
1. If you have LTSC Instaled, log into safe mode, and install the store from the link above. After you are done switch to normal mode and see if the store is working and can deactivate S mode.
2. If your PC came with Windows preinstalled, try that specific windows to see if they can deactivate S.
3. Disable Secure boot (if you haven't) and see if that prevents S mode. I think you have to reinstall LTSC with secure boot off.
4. If windows during setup ask for an online account, try to avoid this and log in with a local account. Better disconnect PC from the internet while setup.
If the above fails...
Either stay with LTSB as it's a 1607 or use a newer 20h2 build made for games.
Wish there were more I could say.