A story we at Flipperescue have heard all too often... I got slammed by TP in a previous thread for suggesting their stencils were wrong.
We have in the past supplied individual stencils ( cabinet front, LHS etc) to customers here in Australia who have bought TP stencils, got half way through a restoration and realised that not only is the artwork wrong but will also never align properly.
It is an issue with those who make files quickly and use what I suspect is "Auto trace".
Flipperescue has always hand drawn their vector artwork allowing for overlay between colours.
Its not hard... just takes a bit of dedication to supply the proper artwork