IMO, this is a flaw that could be easily fixed in the Engine. (I have worked as a technical artist with UE4 for well over a year and am well aware of the problem and the possible workarounds.)
What should be happening is this:
On import meshes named UCX_[BONENAME]01 / UBX[BONENAME]_01 etc. should be assigned to the corresponding bone in Phat (and unassigned bones should get default collisions or no collision and you would make that choice on import). 99.9% of the time I generate a Phat on FBX import only to then delete the default collisions and to generate new ones. I am not exaggerating when I say the system-fix as I am describing it would save me at least 80 hours of work in the next month alone (including the time it would take me to make the collisions in another program).
A basic example where you do want this kind of control, is a complex character, or a vehicle. Your character will need special collisions here and there. Not everything can be handled by capsules. And putting special collisions in your BP is not compatible with Phat constraints etc. And even assigning the capsules would be much much easier in your 3D program of choice.