You will have to.
If you are drilling it on the walls of the porting (or even worse, inside the porting), the chance exists that it will not be able to let air pass onto the chamber since the piston presses the flap against the hole.
When its outside of the porting, the sealing face can flap open somewhat.
It doesnt need to be a large hole
I don't think I'll be able to drill outside the walls of the porting, there will only be about .05" around there.
In that case, your piston may still be too small for the porting.
If you had a larger one (say, 2,5"), you would not only be able to install the check valve hole easier, but it would also perform better.
You COULD make the porting pipe have tapered edges (like a spud-cutter, but then not sharp) this makes not only the sealing face seal better, it also improves flow AND because the porting walls that press against the sealing face are thinner it will be easier to install a check valve-hole.
It also increases initial frontal area somewhat, and since yours is small, it is relatively a large difference.