The first thing I'll point out is that the Phil Bb uses retaining rings, not cups. The Phil design allows for some side to side BB axle location adjustment to best fine tune chain line and ring/frame clearances. It's common to have a little of the retaining rings show past the shell ends. Here's the instructions as on the Phil web site.
http://www.philwood.com/philpdfs/squ...ons_022015.pdf
Here's a shot of one of our touring bikes and it's retaining ring that's not flush with the shell end. Andy