Excellent (or rather, Aha!) this is what I was looking for.
I suspected that there were inherent design limitations in the V-1710 that impeded growth.
Some of the details I summarized there, I hadn't actually seened confirmed until earlier in this very thread ... that said, actually looking at the physical supercharger installations on the merlin and V-1710 ... even comparing the single-stage single speed ones, I'm not sure the Allison engineers could have done much better even with the likes of Hooker's expertise. (the integral supercharger mounting is really cramped and doesn't make for much flexibility in terms of optimized diffusor arrangements, let alone increased impeller size)
The 8.8 and (especially) 9.6 supercharged engines were already limited pretty much to non-turbo installations (turbos were mated with lower blower ratio engines), so universal installation in that regard isn't much of a bonus (unless you're manufacturing nearly identical airframes with and without turbochargers) so the main issue would be standardized volume production ... IF keeping the supercharger/accessories section of the engine even streamlined manufacturing that much. (early V-1710s made some other significant changes like the reduction gearing on the long-nosed C vs short nosed F series)
And given all the trouble that seemed to go into auxiliary supercharger development, I'm not sure simply focusing on producting models that deleted the integal supercharger+carb intake placement entirely in favor of an arrangement that allowed a wider variety of superchargers would have been more practical. (from an engineering time + manufacturing time standpoint)
Pratt Whitney expanded development of BOTH their single-stage (single and 2-speed) superchargers as well as developing auxiliary systems and facilitating turbocharger arrangements ... Wright seems to have focused more specifically on single stage (fixed and 2-speed -maybe some 3-speed) with provisions for turbo installations (though the R-2600 seemed to have trouble).
It's hard to say what would have been the most effective for a smaller firm like Allison ... but most other manufactuers focused on single stage superchargers exclusively until they hit a wall and needed 2-stage (where single stages would have been unreasonably large). That was the situation in England, Germany, and Japan, including implementations of 3-speed single stage superchargers in some cases. (and sometimes single stages + aftercoolers)
2. I seem to recall the problem with the historic Allison two stage engines was that the auxillary supercharger made the engine too long to fit into the Mustang B/C/D/K series airframe without serious center of gravity issue. In the P-51 F/G/H/J series the firewall was relocated further back, and the Allison two stage engine could be installed (as it was on the P-51J).
Same for the P-39 forcing the more extensive redesign of the XP-39E (and P-63). Which again makes me wonder why a side-mounted arrangement wasn't attempted in able to keep the engine length closer, if even at the expense of some drag. (depending on the exact mounting position of the supercharger)
3. Backfire screens are a 'Band-Aid' fix on the real problem, that the mixture to that cylinder is too lean, and the combustion is way late (lean mixtures burn more slowly then a proper air/gas mixture) with the mixture stll burning when the intake valve reopens. I seem to recall reading that the problem with the V-1710-143/145 engine was that the speed density injection system ran the engine too lean causing backfires. Whether than was lack of development of the speed density injector (or as I believe) poor maintenance/incorrect replacement parts, has never been conclusively proved, nor may it ever be conclusively proved.
Backfires related to detonation would be pre-ignition and burning too quickly ... so a bit different /if/ detonation issues were even related to the backfiring ones. (it's possible detonation issues were a separate problem and backfire problems were limited to lean cruise conditions)
Granted, had Allison switched to a direct-injection arrangement for post-war developments that would have changed a number of issues too, backfiring and detonation included, but that's another topic. (just comes to mind with the R-3350 switching to that)
Well... on the Merlin 620 series commercial engines (with an intercooler) on North Atlantic flights, the mixture got so cold during cruise that the engines had trouble. (I assume fuel components condensing out, leading to problems very similar to those seen with the P-38 during WW2). Rolls Royce had to modify the engines to heat the intake charge for cruising conditions. While we like to talk about engines running hard pulling war emergency power, I think in reality even fighters spend most of there time at low cruise power. It could be argued that water injection for the few minutes when WEP is needed might be equal to hauling around an intercooler all the time for the few minutes it is needed.
That also sounds like a problem with ability to regulate airflow to the intercooler ... the same problem can happen with oil and collant radiators (overcooling situations). Radiator duct/flap designs are a big part of this. (along with simply using larger radiator area than needed or operating in colder environments than intended)