Is there any way to distinguish whether this should be "Raise your leg" vs "Raise your foot"?
No, not really.
For me it means "foot", but at the end, I think it all means the same.
What do you think about the following :
If I raise my foot, then (a part of) my leg is raised as well.
If I raise my leg, then my foot is raised as well.
So, it doesn't really make that much of a difference to me.
If someone says something like that to me, then I'll raise my foot.