I will say this, for some of the stretching uses of the stall bars, it helps to have the lower bars be closer together since you can fine tune the progression and severity of the stretch. You typically wouldn't need this on the bars that are higher.
However, imo, as far as structural integrity goes I would make them all the same distance.
If you design your stall bars correctly, you can also use them as a GHD which is very useful. We did floor glute hams near the bottom but I was also able to use it as a GHD with a swiss ball. A bit tricky but it was not stupid dangerous at all.