Those floor grates (holes in the floor) from "Charlie X" were located in the same straight corridor as the transporter room. There are many first season episodes where you see the grates down there by the A-Frame door like in this cap:
You can see the transporter room door behind Charlie to the left in this image referenced above:
That's what I thought. Weren't these vents in the concentric corridors as well? Seems these access gratings were all covered up by the colored carpet stripes in the second and third season.