You, sir, are a fly in the ointment.
I just call it the footy bit. Plural is a breeze.
Ach, quit playing footsie, you lot! 
(With an index finger… 
)
With reference to the OP topic, I call 'em “dummy holes” on a “dummy foot”, though the up-tube one which voices low D is in fact a tone-hole (as are the finger holes, of course). It makes not a jot of practical, acoustic difference which way you point them. I think most folk would kinda automatically align them with the finger holes on assembling the flute, for aesthetic reasons, but it doesn’t matter.
If you play footsie with your index finger, you’re going to have serious trouble with the anatomical complications that inevitably follow upon playing footsie.
Nah. Poking with index finger, not playing footsie with it. Duh! (Stock reply… had to share…)