You are doing it wrong!! Stop!
The non-brake side is large and is meant to "float" as previously described. You install the axle and that larger diameter portion pushes everything over to the brake side.
Then the floating side is left loose and you should compress the forks as much as physically possible while those 2 nuts are loose. While you have all this bushing overlap, the forks should end up being parallel to each other. Have a buddy help. The axle being flush, proud or sunken is not important at all!!!!
So you should be able to determine where the fork wants to rest on the axle, take a mental note of where that is. On my bike, it's sticking out a bit, on my last KTM it was in a bit.
Tighten the clamp bolts only when the fork is running parallel to the other fork. Using it not paralled will cause massive binding not bushing wear, the deeper into the stroke you go the more friction you'll have. Hit a big hit like that and it will stay down.
Good luck!
And if you don't believe me read the factory bike manual on how to re-assemble your forks/wheel/axle.