That's kind of what I do, too.
I think the difference is that because I was able to slide past the aquifer, I didn't have to dedicate a pumper and a mason. They were available for other tasks. As such, I have emptied some of the vegetable bags much earlier than normal (It's about 3 weeks into the game.) I've never had to deal with the case where I have only 1 of the various surface crop seeds AND empty bags.
Did a quick test and looks like the best way to deal with it at this point in the game is to NOT have a seed stockpile at all. Leave 'em on the floor of the still. Still wish there were a way to tell the doofuses not to bag the seeds. Not until I have a handful, anyway.
[EDIT]
Forbidding bags didn't work well at all. When I needed them for the quarry bushes, and un-forbid (claimed?) them the game decided putting seeds in bags was more important than putting leaves in bags. I still have no idea what to do about that. Maybe something with burrows...
[/EDIT]
[EDIT2]
Well, that went over not at all. Having haulers in different burrows doesn't stop seed stockpiles from issuing bagging jobs. It's just now there's no one who can ever do the task, so it just sits there, the seed and bag both locked.
In retrospect, I should have realized that would happen. Early seed stockpiles work great unless you have some empty bags.
Hmm. Maybe QSP seeds onto a tile that can only be accessed by growers?
[/EDIT2]