The upper impulse-shuttle decks are very different on both kits.
On the Clever kit, they are more cleanly and easily fit, as squared-off additions [see pic 1] that glue flush to the rounded deck. The PSF kit encompasses the decks as part of the lower hull fold process, instead of using two pieces, as the Clever kit does. This shaping of these impulse/bay decks is only accomplished by carefully noting this need to bend a framing-difference, as you try to assemble it (no directions makes this effort a trial and error effort) [see pic 2]. Directions here would have made the process far less frustrating. A rough-build is almost needed just to accomplish the desired shape. The good news is, if you do go through the awkward rough build process, the cleverly-thought design makes for a cleaner upper hull shape, when finished.
The impulse engine graphics are better on the Clever kit [see pic 1], as are the secondary, upper support bay doors, and the ones near the stern of the ship.
The PSF kit drops the ball in this respect, creating a glowing refection of the engine, spilling up the hull, not down in the direction of the light flow, and with little impulse engine graphics. The effect is an odd, impulse backwash! The secondary bay is neglected, with the staging area/elevator just folding over where access doors should be [see pic 3]. The aft shuttle bay doors are very poorly graphiced-out as well (and the hull shape is off quite a bit).
These difference in the kits allude to something that I hinted to in the beginning of the thread, regarding the shuttle bay (in TV that would have been called a tease!!). The Clever kit’s shuttle bay is better and more accurately shaped, as compared to the Digi on screen, but it lacks the darker staging area [see pic 4 for the graphic cutaway of the section & 5 for the designer hand drawn notes] between the aft bay and the mid-hull secondary bay access. The PSF does have this recessed upper bay staging area, delineated appropriately in a darker shade. This staging area is provided, at least in print (modification would be necessary to create the layering to make it look better) in only the PSF kit [see pic 3], but as noted before, this recessed staging area bends upward into where a set of clamshell doors should be placed. To build this accurately, the recessed darker ares should be moved a few millimetres toward the aft section, and separate clamshell-doors needed to be added (perhaps stolen from the Clever kit?).
If you look at the cutaway, as provided by the Clever kit [pic 4], the main shuttle bay is merely a deck tall (not high enough to stage a typical shuttle; see designer notes in pic 5) . Only shuttle pods could fit throughout the doors of the lower-stern bay, even with accurate tractor beam guidance [see pic 4]. The upper bay is even shorter than a full deck, making the entry only useful to workboxes (and very rested pilots!). However, if the staging area deck, between the stern shuttle bay and upper shuttle bay, were to lower, the secondary bay area would actually be large enough for shuttle travel. In fact, the entire area could be one shuttle adequately-sized shuttlebay, with a small stern door for tractor launch, an upper elevator staging pad, and an upper set of doors to close off when the elevator is raised flush with the outer hull.
The shuttle would land outside, onto the staging area, and be lowered into the bay and tractor through the upper bay doors, similar to an external elevator system, like the internal one employed by 1701, that was enclosed in the shuttle deck and dropped into the shuttle maintenance bay below the deck.
If this is the "in-universe" solution is as I suspect, then neither kit would work without modification. Clever's kit lacks the darker, shuttle staging elevator, and the PSF kit has it, but it is positioned in a manner where it gets bent when folding the parts properly.
And that's why we do rough-builds!
The Clever kit provides a better hull shape for the stern; it just takes a bit of experimentation to find the right shape. Play with the fold lines before trying to do a quality build, as this shaping is not easy, nor explained in any directions.
The PSF kit is easier to put together in the stern, but the final shape is a bit too narrow and too high; it needs to be broader at the shuttle bay doors.
regarding the graphics in this area...The Clever kit does not provide a between shuttle bay door staging area/elevator. The PSF kit does provide this.
But the PSF kit does not provide upper doors and the darker staining area/elevator elevator is bent when the kit assembled.
At the very least, the doors off the Clever kit would need to be match to the upper deck-bay access, covering the bent portion on the PSF.
The PSF also needs the doors off the Clever kit for the stern bay, as what is printed is not accurate or as attractive as the Clever version’s. Of course, then you’ll have to modify the PSF kit to have its stern shaped a bit differently, or choose to go with the Clever kit, but then steal parts off the PSF to make a staging elevator/pad…