Well there were a couple of locations that looked ideal at first glance, but my tests show no positive results.
Stage 6: There were multiple helicopter enemies just before the boss door. Great, we could probably respawn them and have them fly into the boss room right? Except that just before you reach the boss door, you load a new segment.. a segment which does not contain those enemies, therefore we can't respawn them.
End stages: As already pointed out the first of the final stages, the enemy was 1 pixel away from being useful.
I went on to the stage 4 clone, and was surprised to find out we could respawn one of those flying enemies after touching the door. However, for whatever reason the enemy is stuck in place and will not fly to the right.
Edit: In fact if you shoot and kill it, there is another one there, and this happens infinitely as far as I can tell.
EDIT
I have found one in the stage 6 clone of the final stages. The enemy before the boss door is stuck between a very small pit in the ground and exists when the boss room has loaded. Now all we needed to do is charge our trusty star weapon, since that goes offscreen as far as it wants. Bam, we skipped a boss. Hooray.
Yet another edit
Confirmed boss skip for the stage 7-like boss in the final stages:
The stage 8 clone stage boss is also skippable:
The stage 2 clone boss is skippable, but this one was a bit harder to set up. Basically spawn the wall enemy as late as possible, so that he's still low on wall when the boss room loads. This locks him in place so he doesnt move upwards out of range of the camera and despawn. Then we just have to wall dash up and fire our charged star attack to the left, and the result: