I've ended up using conditions and regular FileSearch in the msi package, it might be a bit annoying that bootstrap installs all prerequisites before msi package and this check is run, but I can live with it.
<Property Id="DEP_EXISTS">
<DirectorySearch Id="CheckFileDir" Path="$(env.WINDIR)\assembly\" Depth="10" AssignToProperty="yes">
<FileSearch Id="CheckFile" Name="Interop.Dependency.dll" />
</DirectorySearch>
</Property>
<Condition Message="Dependency not found!">DEP_EXISTS</Condition>
Works fine from what I can tell.