Ben,
Do I understand what you're asking? You think that, if you put the line tie into the cupped face, it will be down in too deep to tie the line easily?
I have never shaped a popper like that, but, if I did, I'd put up with the hassle of having to thread the line through the recessed eye, instead of putting the line tie above or below the mouth.
Poppers work because they trap both water and air when they're popped, and I don't think moving the line tie above or below would let you do that.
Have you already painted the bait? If not, and you think the cup is too deep, bite the bullet and remove some of the outer lip, so it's not so deep. Having to shave the outer edge again isn't that big a thing compared to making a popper that won't pop.
I put my popper line ties just above the center of the cupped mouth, and then I tie my line and slide it down toward the bottom of the eye to get a really good pop/bloop/spitting action.
I tie line on and cut it off at the Palomar knot several times first, and slide those knots up around the eye, so when I finally tie on the actual fishing line it stays toward the bottom when I'm done. I anchor those knots with some crazy glue. It doesn't hurt the action of the lure.
My biggest fish on a homemade popper is 8.37 lbs, so I know it works. It got me big fish for my club for the year.