I do not know if there is a build in way to skip the repair when using the predefined PackageGroupRef. If you look at src\ext\NetFxExtension\wixlib\NetFx4.wxs you will see how it is defined. I assume you can implement a ExePackage element in your chain, like we must do for .Net packages that do not have a PackageGroupRef (3.5), which has your desired behavior.
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