Ally,
FWIW, I have asked numerours Tour Pros I know and have worked with about that, and they agree with your opinion that once in a while, it's okay. Lanny Wadkins thought about it a while and settled on a maximum of four two level greens per round, providing they were a little different, like side to side, front to back, angled, etc. He thought three level greens were a bit goofy.
As to tie ins, I think TD and I discussed this once. The trick is to NOT just make a straight deck 90 degrees across the green. It should angle slightly to the green edge, and also angle slightly across the green, as well as wobble a bit. Oddly, I learned a lot about doing it well from RTJ (or Rees) at Hazeltine. He probably had 8 two tier greens but you didn't actually realize it at first because of the variety of slopes there.
And yet, so many gca's do build at 90 degrees across the green in a really uncreative way. My old mentors favored that, because they were always on a budget and the 90 degree cross ate up the least amount of non cuppable space. When the tier angles across, not only do you not set cups there, but you are left with a few little triangles too close to the step to set a cup and can end up losing more useable green space.
For that matter, they never did a step the length of the green, always the width to reduce wasted space, but there are some great greens like that. Fazio seems to do side to side steps on long greens, and getting to the pin on the low side (often guarded by a pond, like 9 at Flint Hills in KS) is a great shot - bail from the pond and have a long putt (or chip) down hill with a sloped step and water behind?
MacKenzie did one at UM course on a short par 5 (4th) where there was a grass bank in front of a wide, shallow green, but the green had two tiers front to back. I think where you use a tiered green and on what type of hole has an influence on whether its good or not.