Can I ask 2 questions here, since you are using spot colour. I take in Acro you kept these as spot colours in the separations dialogue. Did you run a Pre-flight check on PDF x/1? I did what you asked and can see overprinting where the lines cross so I cant replicate that at the moment however I did rush it! The line colour shows colour change when I selected "output preview", deselect process colours as it is for spot colours, then select "preview Colour warnings" and the check the "Show overprinting" in the warnings field.