Thanks for the reply @v_kyr, that did the job. I didn't think to check for any fixes in the beta. But that is exactly what was missing from the grid manager, and the isometric studio also is a nice addition. Although I don't know why they didn't just call it axonometric studio. I know isometric is the most popular form of axonometric projection but still.
This formula does seem to solve the alignment of 2 of the 3 planes, but the downside is that the grid isn't uniform anymore, making it impossible to make proportional cubes for example. I don't know if this is possible but it seems to me that the solution is to shift the plane consisting of the first and up axis and the plane consisting of the second and up axis down or up to align with the plane consisting of the first and second axis. I would really like to have other grid types be able to have aligned plane sets, just as the isometric grid type does.