There's no intrinsic reason why there cannot be big jerrycans filled with ketchup on the shelves, where you can fill standardised 1 litre bottles yourself, it's just not how the supply lines currently work.
Actually, there are. It has to do with food safety. Tomato in particular is a sketchy one. Even hippies don't do this, yet they are willing to watch the machine grind their peanut butter to an inferior standard as compared to what's in the jar on the shelf. Honey is also distributed to hippies in the manner in which you describe — honey keeps basically forever, so there is no hazard there. I've also seen olive oil begin to be distributed in this fashion of late. Also, add to the list beer and wine; wine bottle-filling kiosks are beginning to become popular, as are growler filling stations for the beer lovers. And of course, all the dry bulk stuff available in the bins at the health food store, like flour, salt, baking powder, nuts, dried fruits, granola, dried legumes...
Ketchup goes bad easily, so you're not going to see it distributed in this fashion any time soon.
I misspoke when I talked about the environmental impact; what I meant to say was that using virgin glass has basically no environmental impact as compared to recycling glass.