It’s possible to make group policy that only applies to users / computers with Internet Explorer 11 installed. To make a group policy only apply to IE 11:
- Open Group Policy Management and connect to the domain
- Expand the domain
- Right click WMI Filters and click New…
- Name the WMI filter and click Add
- Change the namespace to root\CIMv2\Applications\MicrosoftIE
- Change the query to Select * from MicrosoftIE_Summary where (version > “10”) and (version < "11")
Alternatively (and preferably) you can use Group Policy Preferences, Item Level Targeting.