I figured out a partial work around, if I mentally transpose the sequence to C Lydian and play it that way, with the scale locked to C Major so it sounds right, it can then go back up to C Lydian by changing back to chromatic or changing to G major, all the other modes can be accessed (by staying in major but changing the root note F for C mixolydian, Bb for C dorian, E b for C minor, Ab for CnPhrygian, Db for C Locrian, C for major, G for C Lydian).
The problem where moving C E F to F A B resulting in F A A is fixed, this problem is because C to F is a perfect 4th which can be moved to any position in C except F because F doesnt have a perfect 4th it has a augmented (raised) one. As the sequence is input as C E F# which the keystep corrects to C E F and wherever this is shifted to the augmented fourth will be corrected to a perfect one, except for the B position where the augmented 4th lands on a valid note F, problem is it is not the fourth, B has a perfect fourth in E, it is actually the diminished 5th, which means moving C E F to B will result in B F F as the augmented 4th is not being corrected from F to E as E is a valid note, and the out of scale perfect 5th for B is F# which is being lowered to F. I think this is preferable because at least it moves the weirdness to the diminished chord.
When transposing to different modes this glitch will occur wherever the diminished chord is, as it is the least used chord it minimised the problem, it is most prominent when switching to C Locrian (C# Major) as it the first chord, but as that is a rarely used mode it is preferable to move the problem here.
While this workaround works it isn't ideal, if you transpose modes it does not work well with the auto chord feature. It works perfectly in major, you can set the chord to an extended major one and then move it to different positions, and the relevant notes will be lowered if needed. This doesn't work when you change mode, as rather than change the root note to the new position and then calculating the chord and then correcting those notes, it seems to calculate the chord at the new position, and then corrects the notes that need to be lowered which gives a different result that sounds quite chaotic.