With a spare hole in the roof you can pretty much do anything you want to, maybe first see what the issue is with the windscreen aerial as they do work quiet well, common problems are, faulty fm connector at the back of the HU, poor connection at the drivers footwell connection, no voltage to the aerial amp or bad earthing on the amp, the later sometimes shows up as reception gets worse when you put the heated rear screen on.
Anyway, back to your question, if you ripped out the roof aerial you would also need to install new FM Cable to feed it, as the 2 current feeders to the Saloon Roof location are 50 Ohm cables (one is for the GPS other is GSM) and are no good (wrong feeder type) plus different connectors to whats required for your FM feed. You could if your good at connectors move and or extend the current FM feeder that feeds the Window Amp, or run fresh cable to the drivers footwell (assuming the feed from the footwell is good to the back of the HU).
Another option is to get a FM whip, Amp, and Aerial loom from an Omega Estate and retro fit that setup instead