No, it's not because of the system account uses for installation purposes.
A couple of guesses:
If you are totally on-prem, not Hybrid Intune, then it is exactly what it says on the tin: there are local users for that machine which login, and therefore "some local user" is the primary user of that machine, not a domain user.
If you are Hybrid Intune, then possibly 'who logs in' is an Azure ID, like Vikash.Joshi@YourAzure.edu
Since that is also 'not a domain (at least, not a traditional onprem domain)', CM also sees that as a 'local user'
My top guess because you have 16k like this... most likely you are intune hybrid, and 'who logs in, and therefore becomes the primary user' is an AzureID. one way to check this...
Select count(distinct resourceid)
from v_gs_system_console_user scu
where scu.SystemConsoleUser0 like '%@%'
and if the count is suspiciously close to 16k... then my guess is at least 51% plausible.
The REAL question is... "why do you care". Is there a business process around which you wanted to center Primary User ? What's the end goal? Maybe there is a different way to achieve your end goal, instead of using 'primary user' (which was designed 'back in the day', before Azure IDs were invented, so it's not really meant for that)