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Either design could work, though I imagine it would be easier for you if everything was walk in accessible. So if you like the first coop/run set up, I would see about having the coop built full height so you don't need to lean in to do maintenance or to reach a bird inside/under the coop...

If all gaps larger than 1/2" are securely covered, it should be just as predator proof with or without a solid wood wall, unless you have bears as a concern.