I wouldn't really say that Holy Paladins or Discipline Priests have problems with throughput and they're definitely not trading it off for absorptions. At least for Discipline Priests, I know you can completely forego Spirit Shell and Power Word: Shield and still maintain a comparable HPS to other healers. Overall, I don't disagree with your point about how absorption shields should be designed, but in reality, I don't think that is the case except for heroic modes. In addition, even if an absorption only provided about a 50% buffer to incoming damage (and thus the other 50% could be healed), the latter 50% is also being healed by the absorption healers, so it's not just a matter of leaving the remaining damage for the other healers so that they have an opportunity too.
Take a Discipline Priest and ask them to output their maximum possible throughput for an extended period of time (two excellent examples of where this happens is the last phase of Iron Qon and Rampage on Magaera). Now take any other healer and ask them to perform the same task. I can guarantee the Discipline Priest is going to lag well behind the other healing specs (they might spike initially but once the shields are down their healing goes down the !@#$ter).
This is what I mean when I say "opportunity cost". The only way absorption can be balanced against pure throughput from this standpoint is if the pure throughput of the absorption spec is lower than that of the pure throughput spec (obviously....). Meaning, the absorption spec can stop some of the damage preemptively, but once the shields are down they end up lagging behind. In terms of Discipline this is the reality of the situation already.
That statement really had two parts to it though. The second point involved how much the absorption healers can preemptively remove from the top of that damage. IMO Blizzard has failed miserably at balancing these values. The percentage of this damage being preemptively removed is entirely too high. When you can remove 50-80% of such mechanics from the table only 20-50% of it needs to be healed after the fact. What you said is exactly what happens in such situations. The absorption healer mitigates this large chunk of the damage but doesn't stop healing after it has hit. This leaves very little of this damage to be healed by the throughput spec.
Consider the same situation with the same damage. But, think about what happens when the absorption spec can only stop 20-30% of the damage before it occurs. This leaves 70-80% of it needing to be healed after the fact. This means the absorption spec, with their lower healing output, doesn't suck up such a large percentage of whatever makes it past their shields. Now, the throughput healer ends up covering most of whatever makes it through because they are better
at pure throughput. Yet, at the same time, those absorbs still had their utility benefit because, while they didn't stop most of the damage, they still stopped some of it.
The only alternative is to make absorption specs absolutely amazing at preemptively stopping damage but way below throughput healers for healing it. The problem there is you then have to cripple their healing
output to achieve balance. This alternative ends up forcing a spec like Discipline into being a CD/mass mitigation %^-*!, but terrible at handling every other situation (to some extent the spec is already here, it's just Atonement pushes it a bit above this for a variety of reasons). This just isn't good design.