I understand what you're saying, but...
A simple way to get a feel for the greatly increased distance between keybed and buttons
There is not necessarily any greatly increased distance. For example, one of the boards I was talking about using this way is a Korg Liano, which gives me 88 better feeling keys in a very lightweight package (albeit with no aftertouch). Here is a picture. If you imagined moving the "brains" of the PA1000 forward to where the keys are, there would be just a slight increase in height to the controls, and no increase in depth. Top view and side view:
I only use two controls on the Liano... a volume knob, and a sound selector knob which I only move between piano and EP. I can make those adjustment by sliding my fingers into the small gap between the top of the Liano and the board/module above, I do not need to keep them visually exposed. Assuming I even would be using the Liano's own sounds, which is a possibility, but not a certainty.
having to reach for the top keyboard's buttons, sliders and knobs
As an aside, 99% of the time, all I need access to is the screen (which nicely tilts, for when the board is placed higher) and the 4 Variation buttons (which are at the front-most edge). I use a footswitch for start and stop.
For the sake of experimentation, bring the top keyboard's buttons in close enough that, if the Korg's keybed wasn't there, the controls are where you'd place them while still being able to read the bottom keyboard's display and get to its controllers.
If I'm only using the board as a controller (which is a possibility), the bottom board has no display or panel controls I need to get to, so I can bring the module fully forward as I did on the Liano above. But yes, I may also want to use a board that brings its own sounds/functionalities to the table, one of them being the Yamaha CK61. But its control panel is pretty shallow. Here are pics of that setup, with the full CK control surface exposed. Again, imagine if the PA1000 brain was moved to where its keys are in these pics.
That doesn't seem likely to be problematic to me. But if it turns out it is, I'm not tied to using sounds/functions of the board beneath, I can go with the alternate plan of a controller board for which I would need to access to anything behind the keys. (Or, if I just want to access some sounds from it, access them via MIDI, either from an iPhone/iPad or from the PA1000 itself, which can send MIDI Program Changes from within Keyboard Sets.)
I also have boards with sounds with an even shallower control surface that needs to be kept visible than that of the CK61. If I wanted to use a hammer action on some gig, for example, I could make the board one of the Casio Privias I have, which have control surfaces that are noticeably less deep than that Yamaha's.
For the most part, though, I prefer to stick with boards that are lighter than those Privias... it's a matter of how much I want that hammer action in my rig. I did mention that one of the reasons I like the PA1000 module idea is that, besides letting me choose an action I prefer (in # of keys and/or feel), it reduces the number of heavy-ish pieces I need to bring. The PA1000's 23.7 lbs feels heavier than its number indicates. I think because it is back-heavy, and the angle of the side panels provides no comfortable, balanced grip area.
There's another reason this interest me, though. Besides looking for a preferable action and typically a reduction in the # of 20+ lb pieces I need to haul around, in some cases, I like the idea of 3 boards' worth of functionality. There is no single board I can pair with the PA1000 that gives me quite everything I want, for those occasional gigs where I'm in the mood for some creative excess. ;-) The problem is, if I put the PA1000 on the top of a 3-tier setup (which I did for one gig this year), I feel that the PA1000 is a bit too far away. By putting its "brain" above the second-tier board, I can add its functionality to the rig without bringing a whole 3rd board. I could partially have solved that by using it *as* a module even though the whole keyboard was there (that is, have it up there, but play it from one of the bottom 2 boards), but as you were talking about, that puts its controls a further distance away, and it's a heavier piece to bring, and it starts to look overwhelming for some situations, having 3 full keyboards up there. All I need is the cape!