Perimeters too thin when extruder multiplier is right

Printed a single wall object, adjusted multiplier so the wall comes out at 0.40 mm +-0.01. Since then, I get no overextrusion and negative space is properly sized, but on the other hand, any single line (perimeters specifically) are so thin that they are not even connected.. you can stick a fingernail between the perimeter lines and pull the object apart. Is this a known issue? I am using 1.1.7.
If I increase the perimeter extrusion multiplier, won't I end up with wrong measurements on negative space again? Example: I printed something with 2 nut traps for m3 nuts. The hole was so small, it fit a M2.5 nut, but not even remotely close to fitting M3.
This is no issue with screw holes, but very much so with nut traps.. you can't just cut them open further.

If the perimeter lines are so thin they are not touching, then you are now under-extruding. The issue with hole sizes is not due to over-extrusion, but is a known problem with current slicing software and FFF printers. Until slicing software is improved to compensate (and it is far from a trivial problem to solve), you should design holes and nut cavities etc. to be over-sized - the smaller the hole/nut, the greater the percentage of oversize needed. Alternatively, drill out the holes after printing, or carefully push out a nut cavity with a nut hot enough to melt the plastic.

Dave