Random from what I noticed. I haven't studied it as far as everything you brought up. I will say, I do doubt it's being consumed into my health because I need it after battle and it'll be wiped.
I collect EVERYTHING. I had a whole page of food and it got wiped. So I don't think it was consumed for health because it just wouldn't be possible to consume that much?
As far as the other points you brought up, I haven't noticed a pattern, I just check since it's more paranoid thing now and check random because I've died so much because of it. I can't heal up after fights and be ready for a new one, so I'm having to head back to town to spend bits on food or healing instead of new gear so it's making the game more difficult for me. I think. I do know I'd rather buy upgraded gear instead of food lol.
And no, I don't remember when I first noticed. Takes me a while to get familiar with everything in a new game until it's all intuitive and aware of everything, so it could have happened in tutorial like Mushy Girl but I noticed it for sure about 1/4 of the way through roaming Eden/Paradise Island? Not too sure. But once I noticed I have been checking since.
It's not like nothing goes into inventory, if that helps. It will collect and build for a time. It does show in inventory. But once it's gone, it's ALL gone at once. I can eat and heal just fine if I choose to eat it in the world instead of put it in inventory and I can eat/drink/heal just fine using it out of inventory.
I finally got mad about it last night after I died a bunch over not being able to heal out of a tough battle then stumbled into another one. So I made this post lol.
I'm not trying to bitch. Mostly just bring it up so devs can take a look and maybe patch.