The only definite here is that you don’t stack any components and that you must ensure adequate ventilation.
Other than that the effect of anything you do will be entirely unpredictable. It’s a case of ‘suck it and see’.
Don’t assume that emulating any aspects of Fraim, eg.glass shelves or cups and balls, will have a beneficial ‘Fraim like’ effect on performance. It could just as easily make it sound a whole lot worse.
This is without doubt the most sensible advice here. Follow it.
That doesn’t sound sensible to me.
The OP has only just got the equipment and he describes it as sounding delicious.
He needs to enjoy the music for a couple of months, learn how the system sounds with the various genres he listens too, before he experiments with anything.
Of course he might enjoy experimenting. In which case he’ll have years of fun, rewiring his house with oversize cable, installing a fibre network, buying custom built power supplies with platinum plated fuses. 
The options are endless. 
From the OP:
I wouldn’t be happy leaving two expensive boxes stacked for any length of time either. It compromises ventilation and could potentially lead to long-term issues. I would want to address this ASAP. But that’s just me.
The NC equipment has heat dissipation fins on sides.
If it was critical that Naim boxes aren’t stacked on top of each other, Naim wouldn’t have designed them with flat tops. 
The flat tops are for improved musical performance - not to facilitate stacking. 
Just a few words of caution regarding in cabinet use, heat can be an issue, I ran my av system which was housed in a cabinet and had to fit cooling fans and create many holes in the cabinet and the shelves to allow cool air to flow through and around the equipment.
May not be a concern for the op but just thought I would mention it especially at the moment with our weather being like it is.
Yesterday after a longish listening session my 250dr was putting out a reasonable amount of heat.
I would love to install my setup in one of our cabinets ( out of sight which mrs. S would love) but that is one of my concerns, heat build up but will watch your thread to see how it develops, been some very thoughtful responses so far, best of luck with the project.
Just looked out of interest, the NPX 300 manual refers to sitting (sic) and the shelf being able to support the weight.
The NAC 332 manual refers to installing and includes -
“Never stack Naim products on top of each other, and if you are placing them side-by- side, please leave some distance between the units.”
Here’s the detail of the OP’s cabinet
The spacing isn’t quite enough for the thickness of a second shelf and a box between the existing holes so it will need new ones but there’s the answer to the problem. Another set each side of the existing ones should do the trick, might be easier said than done but no impossible.
To be perfectly honest I think it’s a crying shame to compromise the performance of this kind of kit and at these prices. Rather than buggering about with modifications to something that will never allow this system to perform at anything like optimally I would get some proper racks and be done with it. Maybe build some sort of enclosure around them if they offend the eye.
I know it’s not my decision to make and the OP has made his stance here very clear from the off. I just think it’s such a shame not to reap the full benefits from what is a really lovely system. Just shows how we all think differently and have different priorities and values.
Oh well I’ve said it now. I’ll make my own way out.
I agree that this level of system needs a minimum. Not forcefully a Fraim, but a solid rack, be it wood, with proper shelving to isolate each box from each other. It can be also a wooden furniture rack allowing the side by side set up.
I have seen still worth, with stacking boxes and a microwave powerblock.
This is a obviously a conundrum for the forum grammar police. 
Does that statement apply to 2 items or must there be more than 2?
Normally, more than 1 is already plural, not?
I’ll leave that up to you. I probably wouldn’t have have posted if the two documents hadn’t been so different in the way they are written.
With no Naim, it was just my enquiring mind.
Hi.
I liked your post. The question was aimed aimed at the people who know about these things, I don’t.
Maybe I should start a thread.
Quite a while ago I posted how I had a Naim set up whilst a mate was having building work done. It just didn’t sound right. Strangely he lived couple of hundred yards away, same design house, mains from the same transformer station.
I couldn’t fit Fraim in, can no longer bend and lift like I used to. There is no way I could go to the lengths that people do here.
Having seen the marks from feet directly on cases, heard the interaction of transformers too close together, I accept the received wisdom about not stacking.
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