When you create new site collection (doesn’t matter modern or classic) using Tenant.CreateSite() method you need to specify primary site collection administrator in SiteCreationProperties.Owner property. So if you would check site collection administrators of the newly created site you would expect to see specified user there. However it is not always the case. Sometimes Sharepoint really shows specified user there:
But sometimes instead of actual user account there will be Company Administrator – special user which covers all users in the directory with Global Administrator rights (see e.g. Special SharePoint Groups):
It happens regardless of specified user directory role: it may have Global Administrator role and may not have it:
And even more – if user have more directory roles there may be both Company Administrator and Sharepoint Service Administrator:
I.e. looks like Sharepoint get’s user’s roles and assigns permissions to these roles instead of actual user account. But again – for some user accounts it just adds actual user account to Site collection administrators. Logic behind this behavior is not yet clear so if you have any thoughts on that please share it in comments.