That's some very interesting work by Drexler. I'm not a fan of the visual style of his cutaway, but clearly a lot of thought has gone into it.
blssdwlf, those FP tubes line up really well! I also had trouble fitting S1 Engineering into the saucer, thanks that bloomin' undercut! It's a shame too, because I had a particularly interesting idea after looking at the S1 plans one day; the way that Engineering is located off the axis of the circular corridor led to think - what if there were
two impulse Engine Rooms, one for each "jet"?
The corridor is now a full circle, and there's even room between the Engine Rooms to run a turboshaft! I imagined that this would work extremely well with "full length" tubes, as they could reach all the way out to the impulse housing.
But as you found out, the only way to fit such an impulse engine into the saucer is to lower deck 5 by about 5' and while this could work, it makes for an awfully tall deck!
So, having written off my own layout as undesirable

I'll just address these points:
I'm not so excited about the ceiling being asymmetrical either.
If you go by what we see on the show, the ceiling is actually curved on both sides:
... I can see it resting somewhere on deck 5 or maybe 6 to keep it close to the energizers
What exactly are the
energizers? I know they're referred to a couple of times in the series but that's it. Or more specifically, what is your interpretation of what they are?
After watching "The Naked Time" it also seems that something funky is going on in the curved hallway going up to it.
Could you be more specific? I've watched those scenes many times and what we see seems pretty typical:
The only difference is that they've opened up the radial corridor near the Engine Room to allow Scotty to enter and exit through it.
But in "The Ultimate Computer" we see another long curved hallway (although different.) I might try to work the differences in as a refit in the engineering section on the primary hull.
If you don't mind changing the angle of the Engine Room door, (and raising the ceiling) this is not too difficult. It does lead to an odd corridor layout however!
It also means that you'll need to reinterpret Kirk's stroll to Engineering in
Court Martial, but there's nothing to say that the corridor he walks along is just outside the Engine Room.
Incidentally - does this mean you're not going to have
any Engine Rooms in the secondary hull?