These two things are , to my knowledge, the ONLY things that bag autocollect does not actually collect.
The problem isn't with the item type(s), but rather the delivery method.
Put some commendations and/or heart seeds in your crafting storage and then double click to pull them out... they will auto-collect into your bag just fine.
Something about the NPC 'quest completion' rewards delivery logic works differently than most other item acquisitions in the game. Every once in a while there ARE other things which get dumped into general inventory rather than auto-collecting, but it is so rare that they are easily overlooked. The commendations and heart seeds can happen after EVERY quest in the relevant level ranges.
The fact that they stack neatly in inventory when the bag slot for them is full suggests that what is happening is that the check to auto-collect them in the bag is failing for some reason when there IS stack space available for them and they are getting 'bounced out' to the first empty slot. In contrast, if the bag actually does NOT have room for them then they overflow to regular inventory the way they are supposed to and stack neatly.