The kickout flashing's purpose is to kickout water. In your case it will be at the end of the run. I guess you could seal it. If you didn't have a kickout it would end where you made the cut. I don't see any problems, but a real roofer may come along shortly. I am just a DIY person.
To avoid the "pin-hole" leak potential, I take 2 pieces of step flashings, cut the opposite miter angle on the bottom piece, apply a slight bead of sealant, then sandwich the 2nd piece of step flashing on top of the 1st one with the exact opposite angle of the miter cut.
Or, you could purchase a "kick-out" flashing from a company who makes them.