Usually you can tell if the master cylinder is failing if you pedel is going to floor *somethimes slowly - sometimes fast) when you are braking and basically the car is not stopping as it should!
If the master cylinder was clogged (seals swollen not allowing release of pressure) where it caused that the rear calipers would have locked up, then you would not have really been able to tell other than what you wrote, that the back rotors and calipers were red hot.
As for suggestions, what I would do if I were in your shoes, is rebuild/fix or change out the rear calipers (rebuild is changeing the seal and the piston. Then from there, check the hose that MikeTangas mentioned. If this hose has an internal blockage (like the master cylinder would did not allow release of pressure) that could have easily caused the consistant braking and therefore meltdown/blowout of your rear calipers. If from there, you have not resolved the issue, then go onto the Master Cylinder.
Now how can you check all of this. After getting the rear calipers installed and set up, start bleeding the system. If you are not getting any fluid out the rear calipers or they still lock up, then check the hose. If the hose is not blocked, then onto the master cylinder.......
Also, while checking the system and hose, check the hose for cracks or signs of old age. If it shows signs of old age then you need to change it. Also, if the hose has a bubble on it (I have seen this before) change it. Under extreme pressure and the lack of the release of pressure the hose could develop a bubble - usually near the clamps/fittings and this is not uncommon if the hose develops an internal blockage.
Insanity: doing the same thing over and over again and expecting different results.
2006 - Suzuki Gran Vitara (2.0 L fully equipped) Like this car so far except for trying to put on the seatbelt.
1988 - 190e - 2.3L - 172K miles (It now belongs to the exwife)
1999 - Chevy Blazer LS Fully Equiped - killed it June 2006
2001 - Honda Civic EX - 68K miles (sold June 2004)
1963 - 220S - Dual Carb 6 cyl. (sold)
1994 - Yamaha WaveRaider (fun to ride)