Great post.
As you mention, those lifts shouldn't be viewed as the same and shouldn't be put in the same class. Deep squats are a great way to engage the posterior chain as well as committing proper hip hinge form/technique into memory. If you do a 90/squat with perfect form odds are you will naturally train your body to avoid compromising biomechanics, such as excessive forward lean and/or hip flexion (both can lead to back injuries). For the average Joe these lifts are more important because few Joes NEED (key word) to lift heavy; it's simply for bragging rights. Minimizing imbalances and injury prevention should be the key for this demographic.
Athletes (as you also mention) have an actual need to focus on raw strength improvements (heavier lifts) but also need to build endurance and power (speed). Having a well-designed routine in which the goal of each exercise is properly understood and implemented (at all levels) is paramount. Unfortunately there are many here (like myself) who grew up in a time where it was all about 'how much you could lift'. Thankfully we are getting smarter, coaches are getting smarter, and there is better research/information at our disposal.