Ah damned! There is a new tool inside Affinity V2 !
So seems that will resolve all the problems above ! ( the lateral face of the cylinder etc)
The Shape Builder tool !
video made by NotMyFault with my file! (because i have not the V2 )
https://moiscript.weebly.com/uploads/3/9/3/8/3938813/fullsizerender.mov

So problem stays in Moi for make the same before export the PDF! :) (for the Aff V1)
Make isolated surfaces / Faces / Edges from a 3Dview