So you think it's wise not to ramp up your defense on a guy who's shooting .420 from 3-point land, hope he misses, and hope that Tim Duncan will suck down what would likely be a very long rebound? Bull. Miami had to shoot the 3. Everyone knew they were going to. Every coach with half a brain cell would have subbed in their best defenders rather than putting the emphasis on rebounding.
Either way, Pop had to take a risk, and he just played the smart odds and went with the safest route. It didn't work, but it wasn't the wrong decision.
Your premise is flawed. The rebound wouldn't "likely" be long, it would more than likely be in the area where Duncan could have rebounded it, which it exactly what happened in both cases. The majority of 3pt shots don't end in long rebounds; maybe more 3pt shots end in long rebounds than other shots do, but not the majority of them.
It's not an either/or situation. Put four good defenders out there with Duncan. It's foolish to concede rebounding in hopes of stopping a team from scoring. If you keep giving the offensive team shot opportunities, they
will score.
On the first 3pt shot, Bosh was out, so it wasn't as bad to have Duncan out. However, on the game tying 3pt shot, Bosh was in, Bosh rebounded the LeBron miss in the paint, and passed out to Allen for the winning 3pt shot.
Furthermore, if you are going small in a situation like that, you
absolutely cannot turn the shooters lose after the first shot. On the first play, LeBrons's defender started heading downcourt after LeBron took the first shot, leaving LeBron open for the second shot, because the help could not recover in time. On the second play, Allen's defender followed him inside and but didn't go back out with Allen because the defender got tied up in the rebounding scrum, and the help defense got to Allen late. I don't know if the players in question just forgot what to do, of if this was not emphasized well enough by the coaches when this scenario was practiced, but in both instances, the players did not execute that defensive scheme properly.
IMO, it was poor coaching decision, and it garnered the results poor decisions usually do.