The spindle on a vmc has to be like that so the table can move. But the column is fixed and only the z axis moves. Don't get your designs mixed up, you have the opportunity to build some thing specific to your requirements so best look to optimise it.

If you want to get technical then you don't have to put the cutter directly in line with the bearing but you need to balance the y axis and put its centre of gravity in line with the rails as that will produce the smallest moment loading in the bearings and hence deflection.

I wasn't meaning to use a H beam but rather trying to explain the position of the beam relative to the vertical bearings, ie keep the beam 200mm deep but increase the bearing spacing To 400-500mm. Might need to draw something up.