Run FFXI In Lower Resolution But Scaled Up

Yes, set the resolution in the windower profile to what you want the final size of the window to be.
Then enable Supersampling.
Then close windower, go into the windower folder, open the settings.xml and change the supersampling setting from 2 to a decimal value, for example 0.5
This will make windower halve the vertical and horizontal resolution. So for example a window that is running at 1080x920 will still have that size, but the game resolution will be 540x460 (the UI will be untouched and will still be readable).
I have all my alts setup that way, I never pull up their window anyway.

What Lili said is correct. The supersampling setting lowers the background resolution proportionally, so a supersampling of 0.5 would do exactly what you're requesting by setting the background resolution to 1280x720.

Lowering the background resolution will reduce stress on the GPU substantially, and your menus/scaling will remain crisp. Obviously textures ingame will look worse.

Those of us remembering the old 256x256 and 512x512 resolution options.