I've been pretty unimpressed with how the checkpoints have worked so far, but I thought I at least understood them until now... I'm going to mention some locations in Act II, so....mild spoilers? maybe?

I made it through the Khasim Outpost and through the desert section after that (Stinging Sands?) to the Road to....Alcanum? In any case, I hit a checkpoint when I found a cave in the desert, and I would have sworn that the game checkpointed again when I arrived at the next area and unlocked a new waypoint. I went back to town and left the game. When I resumed the game later, I was back at the exit from the Khasim Outpost. Huh?

I know that all my character progression, loot, etc was saved, and I know there is nothing I can do about the map being erased after I've already explored it (that drives me nuts), but I'd love to be able to quit the game with some level of confidence about where I'll be starting up again. Any suggestions?

Um there's Checkpoints, which means that if you get it then if you die you will respawn there. And then there's waypoints which will be active if you resume your game from last time. But if you reload a game you can't go to the latest checkpoint you were at, only to the latest waypoint. Checkpoint just means if you die you go back there, if your playing hardcore, checkpoint means absolutely nothing.

Best thing is to just race to the checkpoints that have a stone floor waypoint going to town, after playing the game through once it seems that those are more reasonable checkpoints to get to (where there's not a lot of action going on like some of the cave checkpoints that will respawn you at the entrance like you mentioned).

Ok, so that's kind of how I thought it worked... I guess it just threw me off when I clicked "Resume Quest" or whatever and it dumped me back at the exit of the outpost instead of at town, or the that most recent waypoint that I'd unlocked.