Can you explain how you've come to these conclusions? I do almost nothing but squatting for my legs, and it works for me, but I don't see a definitive reason why someone who has limited mobility HAS to squat. It depends on one's goals, right? I think the hack squat machine is actually pretty fantastic for leg development.
Also, why is he not strong enough for 5/3/1? What, specifically, does he need to be able to lift for 5/3/1 to be appropriate? Actually, I'll go ahead and answer this. It's garbage. Complete non-sense. Read what Wendler wrote about how he developed 5/3/1. He developed it when he was OHP'ing 135, following injuries. Which means a 135 max is a fine starting point on any lift to utilize the 5/3/1 template.
I can't figure you out, man. You say things like 'holy shit my numbers climbed,' and yet your numbers now aren't even very good. Particularly in relation to your bodyweight. You talk about what works for you and what doesn't, and yet you've achieved very little. It's great that you've been making progress recently in your own training, but I think your advice is often fairly myopic.