FSharp.Compiler.Tools includes it's own copy of Microsoft.FSharp.Targets, but due to how the current previous (the latest one are ok) fsproj templates are defined, it will always use the system-defined one.
We would need to replicate the changes from dotnet/fsharp#2575.
I'm not a big fan of including package specific logic in paket, but IMO this is one of the few places where it would be worth it.
What do you think?