HTH said:
I don't see it quite that way. The bare root plants will consume nutrients directly from the water which will reduce or eliminate accumulated nitrates. Note: some potted plants, ones with leaves in the water, will consume some nutrients from the water.
I would rather wade in with a knife and trim back plants then wade in to fertilize them. If they do need fertilizer you can use throw tabs which go directly in the water.
I think it comes down to the sort of water clarity you hope, or expect to have. It's true, you could just dump fertilizer into the pond water, but this would undoubtedly lead to an algae bloom which is something most ponders try to avoid. Containing the plants in pots and putting fertilizer tabs in the pots also helps contain fertilizer from leaching into the pond water, which of course will help reduce the chance of an algae blooms.
I've seen you magnificent lilies plants, and relate to your method of growing them, but feel that most backyard ponders might not be ready or equipped with a backhoe like you are for removing overgrown lilies.
( pun intended)
Most backyard ponders deal with things on a smaller scale, and maybe have one or two lilies in their pond and prefer crystal clear water. Yet they'd like to get the best growth and especial biggest blooms from those lilies. I really feel the best way to obtain those objectives is by containing the lilies in pots and giving them heavy doses of fertilizer (in the pots).
On the other hand, if you are willing to manually control plants, especially non flowering plants, then I see no reason not to plant them barefoot in the rocks, I have many like that myself.
I've had, and have, both barefoot plant, and contained in pots or fabric pots. I prefer to keep flowering plants contained so I can add extra fertilizer to the "pots' to get better blooms. The non blooming plants I like to have the roots free to absorb nutrients from the water.