Hehe maybe so? Decker is at the port-side control panel close to the aft port elevator. If Kirk came down the forward starboard elevator then Decker might not see him immediately behind the intermix shaft. Kirk might be scoping out how and where he's going to break it to Decker and after seeing the lay of the land, goes back up and takes the aft port elevator to pop in onto Decker and Scotty. He then steers Decker over to the more private foyer which he spotted on his earlier drop to the main level.
A little wild, but it seems to fit the way the scene plays out, IMHO![]()
I have to agree that (unfortunately) the positioning of the wall and ceiling means Kirk can't really be anywhere EXCEPT the main engineering level. So, like Blssdwlf I was mulling over the reasons why Kirk might want to go down/up/down and I came up with a scenario where Kirk is simply trying to find a quiet spot to break the bad news to Decker.
1) Kirk arrives at the upper level and peers over the railing. He spots Decker and takes the starboard-fore lift down to the main level.
2) Something (or someone!) catches his eye on the lower level and he pauses to gaze over the railing for moment. He then realises that in the meantime Decker has taken the port-aft lift to the upper level!
3) Since the upper level is a nice quiet spot to speak privately to Decker, Kirk takes the starboard-fore lift up to join him. However, Decker was only up there to collect a report from an underling and has now rejoined Scotty on the main level. Kirk sees this shortly after stepping off the lift and moving to the railing.
4) This puts Kirk's back up a bit - Decker couldn't possibly be avoiding him on purpose, could he? Kirk walks smartly to the port-aft lift and rides it down, no doubt cursing the absurdly slow speed of the lifts and wondering if a ladder could be fitted somewhere instead.
5) Kirk does not take his eye off Decker this time until he finally gets to speak to him.
It's a bit of an absurd scenario, but then it's an absurd camera shot too. However, it might explain Kirk's extra abruptness when dealing with Decker, whose cheery attitude would merely fuel suspicions in Kirk's mind that the young captain was leading him a merry dance on purpose. Kirk's terse "let's talk" before leading Decker over the FOYER of all places to publicly demote him would naturally follow; Kirk would have preferred somewhere private to do this, but he's wasted enough time chasing Decker around Engineering already!
...the mystery for me is where did he enter in from on the upper level? If he came in from the hexagon, his entry direction would have been from the right going to the ladder, right?
What I meant was that Kirk came into the upper level using the little lift from the level ABOVE that, the upper-upper level, if you will

It actually looks more like a "3" to me - is is this just a typo, as you described the medical students crossing through "section 2" to "section 3" later in your post?In the Section 4 scene the camera zooms in onto the torpedo just about being loaded, in the next shot the camera zooms out. For one second in both of these scenes we can actually see the left half of the docking port number - it is a "2".
Having "bays" be more like "sections" solves quite a few issues, although it is a lot of sections for such a small area! I wondered myself if Bay 4 might be the aft launcher, and since the "photon exhaust port" is never explicitly called out as such on screen, it makes a perfectly fine launcher IMO.
Here's a publicity photo with Grace Lee Whitney standing in front of the fake extension which appears to consist of only six corridor wall elements.
A lovely pic - and very informative too! Those wall sections look like the smaller type (approx 4' wide) so it reduces the overall length of the extended corridor considerably!