The thing that has worked over here is that one section of the yard is "no chickens allowed" by means of fence (lattice in some places for looks) attached to the house if you see what I mean. We've chosen to have the front of the house and both sides as NO chickens, available for vegetables, as well as the berry bushes, lots of perennials, etc.
The back yard, only, prob about half of the property, maybe less, is open to poultry. They stay in their run in the morning, and we let them out for about half the day, if possible, or when the kids gt home from school. That has cut down on insae amount of poop on the chairs, etc, while still letting them get plenty of greens, and letting us enjoy how beautiful they are when ranging. They still go home to the coop on their own around sundown, and then we lock em in.
btw, for some reason, they dont seem to bother purple spiderwort, which is technically a weed but is about my fave flower. So you could put nice clumps of stuff like that where they are allowed just to make it pretty and all.
I should say that we live in town and this is not a giant lot by any means. The point is we havent had to fence off the flowers, which would make no sense, I agree, if you're really a gardener. We just fenced off a giant area, built to the sides of the house, and made that chicken land.
Works for us.