My contention is that, given I own an SH or SJ, and have the money to spend I would prefer a lifting system that does not compromise the clearance under the rear diff and should, at the same time, rectify the design of the rear lower control arm that unnecessarily reduces clearance closer to the wheel.
I do follow you; you make good points though the exhaust cannot be excepted from the clearance measurements (lowest...except exhaust).
Here is how it was on my 2013 Outback.
0.5" spacers and 0.4" from bigger tires. Total 0.9" lift. No rear subframe drop. Then skid plates under engine, transmissions, and rear differential.
Outcome, measurements: real life clearance to front and transmission skid plates: 8.5". Clearance to exhaust: over 9". More to rear differential.
Outcome, driving: no issues on easy trails in the US Southwest, constant ping-pong but few real hits when driving carefully on moderate 4x4 trails. Note that some moderate trails where too hard to even try. This due to approach and departure angles on the OB. Some also test the AWD to its limits.
2" spacers, 2" drop, 0.4" from bigger tires. Total 2.4" lift + same skid plates.
Outcome, measurements: 10" to front and mid skid plate but note that rear diff is now only at 8.5". Therefore the nominal gain in clearance is 0".
Outcome, practice: WAY easier to drive moderate trails in the US Southwest even though some remained too hard to be worth trying because the only Subaru with half-decent angles is the Forester. No lift can salvage the approach angles of OB, XV, Tribeca, or Ascent. Also, some have ledges where the AWD is out of its league.
In sum, there is no reason to be too worried about the rear differential becoming the lowest point. I only hit its skid plate hard once, and I knew it was coming, so that was on me. I went too fast through a very small but deep mud hole.
Also, I NEVER had issues with the rear control arms. There was a guy with a heavily modified 2015 OB who broke one of those, but that's because his car was too heavy. Judging from his videos, he was not as cautious with the skinny pedal as I was.
On the contrary, the Toyota Prado design's weak point is precisely the rear lower control arms, both their mounting points, which are weak, and the arms themselves, which are weak as well. I have scraped one of mine already (the 4Runner has the same frame/configuration as the Prado) and one of my rLCA skid plates took a good hit on a very remote and long track, just 20-30 yards from the very end! That hit would have deformed the mounting point had it been still unprotected. But I never ever scraped the rear control arms of the OB and I did plenty enough to doubt that is an issue on a Subaru. Yes, they are a sore point visually, but never had an issue.