Sorry to not have answered sooner.
They are correct that each individual hospital in a system must apply independently for Magnet. Very few systems do this because of the cost so they generally choose their flagship hospital to try to get Magnet status for. The hospitals can vary widely in work environment as well as policies within the same system so you definitely need to evaluate each hospital separately and not go by the fact that it is part of a larger hospital system.
I've now moved well away from the area so I don't have any great places to refer you to. And where I am now has been a lot worse than the facilities that I worked in down near you.
The complaints that I heard from several nurses that worked at those hospitals were the general complaints that are common everywhere. That makes it hard to see if there is really a big problem at one hospital versus the other. None of them ever had anything spectacular to say about either place.
Make up a list of specific questions and ask both places the same questions to see which sounds better. You might also ask to speak to staff nurses on the floor. After some interviews I would go up to staff members throughout the hospital on my way out the door and ask them about their job and the hospital. You can get some interesting answers because they are so shocked that you came up to them out of nowhere and then they say the first thing that comes to mind, which may not be what the admin of the hospital would want you to hear.