Your comments jog my brain, and this one was brought up by Jon Beyle from the beautiful state of NC. Has a pigeon toed athlete with tight hip flexors and planus feet. By the time the ATC gets to her, she can't squat or lunge without pain.
Usually (not always) this scenario is a result of some combination of femoral or tibia anteversion. It's frustrating for the ATC & athlete alike. Naturally, there is nothing you can do about the skeletal configuration. However, you can address the soft tissue issues that go along with it. The femoral rotation creates what Janda called "pronator distortion syndrome" (you should be able to find some references to it on the net). Lots of passive ROM & myofascial work, especially about the hips, is in order; as well as remedial PRE for the abductors, external rotators, and extensors. The athlete must understand that these exercises must ALWAYS be included in their warmup/conditioning. An orthotic can be useful here.
If lunging & squatting hurts, then don't do it. Mini-band work may be a better option. But usually, you can play around with squat depth & foot placement/angle/rotation so you get a pain free squat or lunge. A lot of cooperation on behalf of the coach is also needed; reducing the amount of sagittally oriented running activities.
2 years ago I had an athlete with a similar problem. He did football & track. Chronic knee/low back pain. FB was manageable, since most running is multi-directional. However, once he got to track & field it was another story. It took a lot of ART & passive ROM work on my part to keep him pain free. We also did 2 workouts per week in the pool. He's in college now, just doing football, and for the most part is well. As successful as he was at it, I doubt he could have continued his track career.