I am happy to report that we recently published Scanner for .NET v9.2, and then v10, that specifically aims to solve the use case of custom certificates. That being said, please use v10 as v9.2 has been deprecated because of a security problem.
You can read all about it in the announcement for v9.2, but, in short, it should cover existing use cases that were working with earlier SonarQube versions.
It will also allow you to now store certificates in a local trust store an not require having them in the machine’s certificate store, if you so wish.
An updated Azure DevOps extension will be published in the coming weeks, but in the meantime you can use the latest version of the tasks and manually specify the scanner version, if you want to test this version of the scanner or adopt it early.
Please give us your feedback on this version and let us know if you still encounter incompatibilities.
Denis