so, to reference how other isomorphic keyboards (eg Push) do custom scales: on Push, each row goes up in fourths still, but rather than each pad being a semitone, each pad is a step in the scale. Ie: seven pads horizontally for the seven steps of the scale before the octave comes around, upwards in fourths. If the scale is less than seven notes - blues, pentatonic - octaves come more often.
Push indicates octaves with highlighted blue pads for octaves, and highlights the current notes in green - across all rows, ie, if you push a note in row 2 that is also in row 1 and 3, it will light in both of those.
Anyhow: isomorphic layouts with non-chromatic scales work really well, although the small key size on a grid makes the chromatic layout much more playable than on a Push.