

Can you share your schematic?
Burying wood 2x4(even GC-rated PT) will shorten it’s life by a whole lot. If at all possible, I’d alter your boxes to have something like stone, concrete or synthetic for the ground contact and use cheaper wood once you’ve made it above ground.
Regarding the flagstone, usually there’s a lot of prep that goes into laying stone, including digging down some inches, and using some substrates that are tamped/packed in before placing the stone. Then you’ll usually like a sand or similar in between the stone to key or lock it all into place.
That’s not to say you can’t do it the way you’re describing but be prepared for some challenges in maintaining afterward if they shift or sink.
How much shorter depends on a lot, like moisture content, ground composition, stuff like that so I couldn’t say with any precision but I’ve seen PT wood rot to disintegration in less than a couple years. You could just kick the top of the piece and it just crumbled.
There’s options for you if you’re set on burying wood-type construction. Take a look at PVC or trex-style decking planks and see if you can design at least your uprights, corners and bottom boards in that material then if you want(for cost, probably) switch to wood when you’re a foot off the ground.
Regarding your stone, I understand the moss is a part of your wanted design and I think you can build it in a manner that you could use it. Like I said, just do your best to keep gaps to a minimum and pack as tightly as you can.