As splitters/mergers can by now be stacked on top of each other what you can do is:
Don't start with the belts and add the splitters afterwards, but do it vice versa instead.
So if you want a splitter on a level above ground, first build one directly on the foundation, then build more splitters on top of that one until the desired height is reached. Afterwards, you can dismantle the auxiliary splitters and you have a splitter floating in the air. As soon as belts are added, it will look just like before, but now with guaranteed perfect alignment snapped to the grid.