I will say the "bump" is likely 1/32" so the real issue is just the very small distance between the edge of the flange and where the holes where drilled. (I wish they just made a larger flange as I can see no reason why not).

Would you suggest #6 3/4" screws?
#8?

Drill small pilot and then screw in?

It was suggested to use #8 bolts but I do not see a way to drill that large a hole and still have any real material left of the nylon beam.