What actions save checkpoints?

Other than the regular progress checkpoints, are they any other actions that trigger a checkpoint? Picking up a Praetor point? Completing a rune trial? Using automap stations or other stations? It seems some actions only save your status, but don't give you a checkpoint. E.g. if you pick up an Argent cell and use it to upgrade your ammo, all your weapons will have increased clip sizes and be given full ammo amount. But if you restart the previous checkpoint then, you retain the increased clip sizes, but your ammo amounts are the same as before, and so is your position (i.e. no checkpoint save in that regard). I'm asking because I surely want to know what actions create a true checkpoint with saved position, status, and inventory, so I will be sure to perform it last before I need to save.

Checkpoints are different from upgrades. Checkpoints are where you spawn in the level as you progress, while upgrades are universally kept. There appears to be no level serializer so the checkpoints themselves are kept somewhat vague and independent in terms of progress.
This also means everything runs in a perpetual NG+ mode. Anything you find in a current run is immediately available if you go back to a previous level.

Strangely, even in [Ultra-]Nightmare, checkpoints are indicated even though they are never used.