When you delete a managed package from VCS by deleting its <InstalledPackage>, Gearset should look for all traces of that managed package in VCS and delete those files/update the metadata

The <InstalledPackage> file identifies the namespace - eg. SomePkg, and Gearset should be able to remove files that start SomePkg__ as well as delete/edit metadatablocks within other files that reference SomePkg__c.

It is extremely tedious to remove managed package metadata from VCS otherwise; especially if the customer opted to put a lot of managed package metadata in VCS (perhaps by accident)