[Linux][Bug] UBT Generating paths that do not exist for include search path

I am writing the KDevolp project file generator and KDevelop started complaining about missing include paths that UBT generates. I don’t know if this is normal or if UBT is broke. I could ignore it, with checking for its existence with Directory.Exists(ThePathToCheck), generating the .kdev4 file but I don’t know if this is causing other issues in other platforms or projects or if this could cause some serious issues down the road.

Here is a list of paths generated that do not exist.
https://gist.github.com/salamanderrake/cd655fcfea18043f472d

Can be marked as fixed/invalid