Regarding the different rail options you mentioned: My vote would be to use a 1/2 (or 3/4") EMT rail + bearings (similar to the Artisan3/PlasticMonstrosity) but with two changes:
- Only use one rail for the Y axis and keep the skate wheels for the opposite side. With only one rail you don't have to worry about over-constraining the axis motion and having the gantry bind if the rails are not perfectly parallel (or if your table swells from humidity).
- Use a 2-bearing rather than 3-bearing roller design. This allows you to mount the rail directly to the table because there is no clearance required for the lower bearings. It also leaves the top of the conduit clear to drill+screw through so you don't have to get cute with how you attach it. Finally, the weight of the gantry will be more than sufficient to resist any upward, sideways, or torquing moments the the tool would be able to create.