Q: Does Runecast offer the ability to ignore certain issues and note down the reasons why an issue is not relevant to a specific setup?

[Runecast_Admin]

Yes.
The ignore feature is available for every single issue, either from the issue itself or through the filters view in the settings, which can be used to exclude issues from views and reporting. The annotation feature is available for every single issue to document the reasons why it might not be applicable for your environment.