If the line was pinched enough to block the flow of fluid, and this kink or blockage was not alleviated when the bike was in your shop and the brakes were being bled, should you not replace that line? I understand that weighting the brake pedal 'reinflated' the squeezed brake line, but might this kink have weakened it? Perhaps to the point that the line will rupture at an inopportune moment (like when you are braking) and spray brake juice on the tire?
I seriously doubt that weighting the brake pedal "re-inflated" the line, it sounds more line the caliper was loose, since the stopper bolt was loose, allowing the caliper to move just enough to bind the rear unit on the sliding dowel causing the rear brakes to drag. Movement of the rear wheel (rolling the bike) probably wiggled it enough to cause it to shift and settle again and appear to work, until the brake was applied, thus causing the unit to move and jam up again. As far as the rear brake line, It goes underneath the caliper and is routed close enough, that the caliper may have pushed up against it to impede the flow, or the piston may have caused the flow issue as well. The reason to weight the pedal after bleeding the system is only to allow micro air bubbles to purge over night.
As far as trouble shooting the entire brake system, I must say our Kentucky friend had ALOT of patience and never gave up! We eliminated possible causes, step by step, over the phone, late at night, when he was very tired and frustrated...but he never gave up! He has my respect for sure.
I only led him through the things to eliminate, he found the loose stopper bolt on his own....thus, I dub him the Kentucky ST Whisper'er.
Igofar