Skyler had no idea where he was and he was able to come up with a cover story.

It's been too long since I've watched that BB episode to know if there's a deeper statement in the parallel. Like you said, Jimmy endangered Kim by being honest with her about stuff she shouldn't be involved in. Was Walt protecting Skyler by hiding the truth from her? In a sense, obviously. That was Walt's logic (or purported logic) throughout the entire series (and logic that Jimmy echoed a couple episodes back about his Mesa Verde maneuver). But I don't remember enough details of that particular BB episode to know if they were trying to draw a connection.

Did Saul ever forcefully tell Walt that he couldn't let Skyler get involved in his business? I think there was some of that but I don't remember how much. The interpretation I'm leaning toward would obviously be a retcon, but it would be an interesting one.

This is all pretty standard 'film noir' stuff, but it's fun to see how skillfully they're working it all out.