The issue is not about remembering that one row is samplers and one row is AUs (and in fact they're not, they are in columns!). The issue is being able to FIND the right key quickly.
Using an analogy, imagine if you're playing the piano and you see the chord "C E G" on the staff. Now suppose you wanted to play in a different octave but those notes were in different places in different octaves....you would go nuts!
Indeed, if you're playing the guitar and you want to transpose to a different key, you can slide up the fretboard and the desired notes are still in exactly the same relative locations so you can play the sequence "1 3 5" wherever you are (vertically) and get the same result. I'm suggesting that the same should be true for the Alpha for control purposes.
As for playing notes on the alpha, the situation is even worse because the actual scale can change, i.e, the note generated by pressing a specific key can be different depending on what you're doing. If you're told to play key 17, how can you possibly know what physical key that represents when it can be different depending on a particular layout, and even worse if not all keys in a column are used.
Indeed, it might be worth thinking about using a cartesian notation for absolute references.
(3,1) means 3rd row, first key
(5,4) means 5th row, fourth key
(24,2) means bottom row, second key
That scheme would work across all Eigenharp instruments consistently, making it easier to switch from one to another as well.
The key number that makes the most sense to me, follows the flow of the notes, ie. higher is vertical. In the case of the keygroup mode layout, I personally don't remember this at all with numbers, I remember that one row are sampler instruments, the other row has AUs, than the three natively modeled instruments and then the MIDI outs. The final row I just know by hard.
Also, this logically groups together functionality in lumps of consecutive numbers, which does feel easier to understand.
Of course, this is all very personal but it's interesting to see how people have different views of what looks like the most logical approach.
Take care,
Geert