There are 2 parts to how the MS Di Abstractions and Container are working in Sitecore.
1: The Configuration
The config/configurators etc.. don't actually do the registration of the types with the container. Rather, they just add the required registrations into the IServiceCollection which at the basic level is just a collection. Nothing is done with that ...
Sitecore support asked if I can just change over to use the built-in Microsoft DI, and gave arguments that it is faster and better supported by sitecore. They mentioned that this 197841 may fix the issue. At the time they didn't have a release for 9.0.2 ready, but it looks like it's up now. Instead I bit the bullet and changed over to Microsoft DI.