Jasper Jig can use any size shank/cutting diameter. The measurements are calibrated for 1/4" but it's easy to add or subtract to convert different size bits.
I use a 1/4" spiral upcut bit for cutting standard circles (the spiral is a little better than the standard fluted straight cut bit). For subs, most people just use a double baffle arrangement where the outer baffle is cut to the basket diameter and the inner is cut to the mounting diameter. The outer baffle provides the flush mount (it's usually not going to be perfectly flush but will be close enough).
For true flush mounting (usually for smaller home audio speakers) I use a 3/4" mortising bit.