I think that the 6mm D shaft should fit, but I’d look for the ones without the indicator line. Usually, you only want that kind of marker on a master volume knob. Most encoders are “endless” making the indicator just a point of confusion.
I’m pretty sure that the flat spot at the bottom of the D shaped shaft will act as a buffer zone and prevent that, but even if it didn’t, they don’t make the interior of these knobs very deep.
The height of the top of the knob off of the deck will depend on the overall knob height and won’t impact the amount of travel. Since only the inner hole diameter and not the depth is given, contact the seller if you’re concerned about it, they can probably provide a measurement for you.
Elektron support can also sell you another factory original knob set if you email them through the support link on the website, so just another option.