TLDR: When not focused on a spacecraft and it drops below the critical height for despawning, check if the weight is less than X*deployed parachutes + Y*deployed Mk 25 parachutes. If it is, let it land safely. I was attempting a 100% recoverable run now that 0.21 is here, and was confused when with two identical rockets, one's main stage splashed down safely as I watched it, but the other appeared to have crashed. Looking into the matter, this was apparently caused by a bit of shorthand used by the game when a vehicle doesn't have focus. Since this is obviously quite a setback for my plan, I was hoping for a kludge that would guesstimate whether a despawning object had enough parachutes to land safely (say, 1 ton per parachute for Kerbin). If it is, find the center of drag/center of parachutes and the center of mass, and declare that it landed in an orientation with the former directly above the latter. This would not be intended as a substitute for a controlled landing so you could set the numbers lower to err on the side of failure, but it would be nice as a way to let us land boosters and fly our rocket at the same time.
If it was me, I'd add more pools of Science points, and allow a single event to draw from multiple pools. Instead of a single Goo pool of 10 points, split it into two pools of 6 and 4 points. If you retrieve the Goo this counts for both pools, but transmitting data only accesses the one pool.