I've used BK bearings (similar to FK but in block format) both ways around depending upon package space with other parts of the machine. Didn't notice and problems from doing this.

I assumed that angular contact bearings could take equal loads in each axial direction therefore it didn't matter. But thinking about it I guess one face of the flange/block could be more accurately machined 90 degrees to the main axis? But don't know for sure.

If both faces are 90 degrees to the main axis then I can't see a reason for not connecting it the other way around if you need to.

You could also build it the 'wrong way round' then use the CNC machine to make new bits including the clearance hole to mount it the 'right way'.