The three header (connector) pins point upward when the PCB is located in the printed holder.. so far so good. However where the pins then turn at a right angle and pass through the PCB they then appear to touch the printed holder. Does this matter?
It doesn't matter, you won't short circuit the PCB if that is where you are afraid of. The back of my PCB was also touching the printed part.
I don't expect that the three header pins will be shorted as the plastic is a good insulator but it's better for them not to touch. As there is no restriction on the size of the printed part then making it 3mm larger or making the internal hole bigger by 3mm is a way to avoid a future problem where the part does not quite fit and the PCB is bent.