I don't do any structural so am probably shouldn't answer...but, couldn't your view be fixed with View Range?

OK I solved this pretty good. Thanks Dave Jones for your effort too. Here's what I found if anyone's interested:

So when I began modeling these joists, I set a reference plane at the bottom of the roof deck, as the top of the joists would be at that level. But what threw Revit off was that the steel beams were 2 1/2" below that (the joists have a seat at each end that is 2 1/2" deep)

So even though this seemed logical to me, Revit didn't like it. So all I did was lower the joists' reference plane from the bottom of deck to be at the same height as the steel beams, and then added a z-direction offset of 2 1/2" to all the joists. In the real world, it's the same thing and maybe 20% (ok 10%) less intuitive than the one that actually worked. But now the joists have that beautiful cutback and they look right in the model too. Oh and I overrode the graphics in view so they didn't look so thin in the plan.

This is one of those things where I would say "why does it matter?" I guarantee you that whether the joist line touches the beam line or doesn't touch it, it will still get built EXACTLY the same. I sure wouldn't want to go around having to set a 2 1/2" Z offset to ALL joists on the project, unless you're referencing the top of the beam as your main joist bearing datum.

It's totally exactly how joists are supposed to show up on a plan. It's not rocket science. In fact Revit does this by default for wide flange beams really nicely. But for joists it doesn't. But I figured out what Revit wanted for things to look correct. And it's easy to select all joists in this and lift them up 2 1/2", so things worked out nicely.