I think I know the two 4-note phrases you're referring to, and no, they aren't identical.
Again I'm using the Virtual Piano applet to list the notes, and I'm not sure I've got the right key; I'm only going for the pattern here. The "Enemy Within" motif is two descending intervals, a perfect fourth and a diminished fourth, then back up nearly an octave to the first note: C-G-C#-C. The "Enterprise Incident" Romulan-ship motif is a symmetrical one, a falling half-step and a rising half-step: G-F#-F#-G. They really don't have anything in common beyond having four notes and ending on the same note they start with, and sometimes having the same staccato rhythm (although the Kaplan motif has more variations in how it's used, as you say).