Looking at the percentage spacing of points used in Cube Based Characterisation, for Cube sizes 3 through 10, for Legal 10 bit (leaving out 0% and 100%):

3: 46.69%
4: 29.91%, 64.04%
5: 21.80%, 46.69%, 72.83%
6: 17.01%, 36.53%, 56.96%, 78.20%
7: 13.93%, 29.91%, 46.69%, 64.04%, 81.85%
8: 11.76%, 25.23%, 39.38%, 54.00%, 69.06%, 84.36%
9: 10.16%, 21.80%, 34.02%, 46.69%, 59.59%, 72.83%, 86.30%
10: 8.90%, 19.06%, 29.91%, 40.98%, 52.40%, 64.04%, 75.80%, 87.90%

It's clear the points could be more uniformly spaced, but aren't. What's the rationale for why they aren't?

All I can say is the spacing is very deliberately not uniformly spaced.
But, as you can make any patch sets you want, you can use any spacing you want.

Steve

Given that the spacing is the same, regardless of Gamut/EOTF, that seems like very little rationale.

Please feel free to use any spacing you want.
That is one of the beauties of ColourSpace - you are not restricted to any given patch set for profiling.
As with most of ColourSpace operation, there are no set restrictions.

Steve