My drill isn't a stock unit and I still have that problem. As far as I know you're stuck unless you either have a wider machine (5x10) or you mount the drill next to your spindle (on Y) instead of to the left (on X). If you mount it on Y you're not going to be able to drill everywhere on the table.

This new shoe I made actually works awesome. It's far easier and faster to print too. I'll clean up the files and post them soon.