There are two trains of thought here and it comes down to which is more important, reach or throat depth. With the fixed C-beam/moveable gantry approach the effective throat is the full depth between the work surface and the bottom of the C-beam end plate. So assuming that dimension is 2", you have to have a bit extension/router extension that will reach all the way to the work surface. Long bits or hanging the router a great distance out of the mount are not a good idea though. With the moving C-beam axis the bit will naturally be set extending below the C-Beam bottom plate as the bottom of the collet is generally set at the same elevation as the bottom plate. While the bit can easily run down and reach the work surface, the extension of the bit below the bottom plate reduces the available throat depth. So for a 2" overall throat with the bit already extending 1" into the available throat, the maximum you can cut all the way through would be the 1" remaining. Sure you could choke up on the bit to where it only extends 1/2" allowing 1-1/2" throat depth but then you can only mill 1/2" into the surface. Functionally the usable throat depth will never be more than half the available which in turn causes builders to jack the X beam way up to compensate which is never a good solution.

Personally I prefer the fixed C-beam as the available throat depth is always there. If you're cutting something soft where long bits are acceptable it's already good to go. If you're cutting something hard and thin, simply put some blocking on the platform to bring the work surface up to where the bit is within easy reach.