The spine is the foundation isnt it? You cant stabilize properly if the T-Spine is stiff and if you cant create stabilize properly your shoulder/hips will develop issues which would cause a downstream effect wouldn’t it? My understanding is that no matter what you do to your ankle, it’ll still have issues if the hips are wacked – but if your hips are good it’ll atleast put less pressure downstream to the ankle allowing better positioning, which may not be the issue but why try to mobilize the ankle if its unable to get into a good position anyways. I’m not saying your PT is wrong, that’s just what my take on K-Star’s work is – which my interpretation could be way off. 

I have the same kind of issue, when I’m laying on my back with my legs straight and raise my legs above 45degree then lower them my right hip clicks – no pain, just a loud clicking sound from what I believe is the tendon flicking over the hip (at first I thought it was my hip popping in and out because my leg would ‘shake’ when it flicked as if it was slipping in and out). I found that I’m extremely tight anteriorly in my hips and once I started to work on that (smashing of the TFL/Psoas/IT/Illiacus, Banded Hip Capsule work, Super Couch) then the click would either be non existent or very slight – I personally think the smashing of the TFL/Psoas and Capsule work has been the most benefit tho.  

I’m not sure if this is the same issue as yours or if what helped me may help you as well as mine does not ‘Click’ when I’m standing and try to perform the same action