Before I did anything further, (including riding the bike) I would remove all 3 calipers and clean/inspect all the moving parts (piston's, guide pins, retaining pins, rubber bits, etc.)
We know from your pictures, those are NOT OEM Honda pads on the rear, and the rear pistons are beyond dirty (see binding/scrape marks on piston in picture).
This alone may explain why you have to push stuff back manually etc.
Remove the pads, clean everything up, and inspect all the bits, then post more pictures.
You need to inspect the rear caliper mounting bracket carefully, as most folks miss the minor damage that may be causing your brake issues.
Your looking for flute like wear in the bracket hole (think sand waves) a loose front clip, allowing pads to tilt/bind, dirt obviously, and pad fitment issues.
Those pads are missing the heat shield behind the cage, which may be throwing off the fitment enough to bind/jam.
You stated that your SMC appears to be working correctly, but don't be so sure just yet.
If you grab the LF caliper, can you shake it forward/rearward and cause it to make noise? (dead space inside bore)
Its possible that air in the system, weak/worn assist spring, worn rubber scrubbers, will still allow you to forcefully push the piston down enough to lock and seem to release the rear brake system.
It should take very little effort to preform the safety test, but you can get incorrect results with brute strength etc.
I've seen folks push so hard, they almost push the bike of the Center Stand, and because they were able to stop the wheel, they thought it passed the inspection etc.
I would also loosen the stopper bolt, and the rear axle nut, then re-torque them in the proper sequence (stopper bolt first 51 ft pounds, axle nut second 80 ft pounds) verify in your service manual.
Also check the condition of the guide pin(s) in all three calipers.
A dealership missed this one (trying to attach photo below) after replacing all the lines, complete rear caliper, complete SMC, levers, fluid, labor etc.
Cost the guy a lot of money....when he bailed on the shop and brought me the bike, I found this!
![20170605_140149_1591570932141_001.jpg 20170605_140149_1591570932141_001.jpg](https://www.st-owners.com/forums/data/attachments/142/142054-e1136b8437b1ac54f900c0caadca46ef.jpg)
![20170605_140356_1591570931362_001.jpg 20170605_140356_1591570931362_001.jpg](https://www.st-owners.com/forums/data/attachments/142/142055-32ee4bf7a2b621761da6a0d85d63470d.jpg)
![20170605_140133_1591570932810.jpg 20170605_140133_1591570932810.jpg](https://www.st-owners.com/forums/data/attachments/142/142056-f0758b25654f74d4a63732f720c5f998.jpg)
![20170605_142343_1591570928078_001.jpg 20170605_142343_1591570928078_001.jpg](https://www.st-owners.com/forums/data/attachments/142/142057-4a460a7a06274ab3ed2fbbb9263a80dd.jpg)