I think there is a misunderstood of the product here. You will call the SSIS IR only via the "Run SSIS package" activity and there you would specify your SSIS package location.
Please have a look at the following article : ssis-azure-lift-shift-ssis-packages-overview
So regarding you points:
1 - Linked services would be associated only with Azure IR (AutoResolveIntegrationRuntime is the default Azure IR that comes with ADF deployement) or Self Hosted IR
2- Is public access denied for this file storage, because default Azure IR would use public access
Hope this would help