Supposedly, Secret of Mana uses direct color + mode 3 for one of the world maps. that's a good 20+ hours of gameplay to reach, though.

It should work the same as mode 7, except that mode 7 doesn't have 3 palette bits in the tilemap.

What modes are those last two shots actually in? The first one is obviously Mode 7. The second very well could be (possible logo tricks like Actraiser pulls). The third would be... strange. That looks like a classic place to use Mode 3.