A bit of an update:
1. My Prodigy Commander went back to the mothership, where they reamed and polished the barrel. My guess is while it was there, they simply checked to see if anything was out of factory spec, and then corrected it if it was. I also think that this had nothing to do with my malfunctions, since none of my failures to feed managed to get the round chambered. It does make me wonder if they even bothered to test fire it, though. Still, it was nice to have that fixed as a known issue.
2. I think I managed to fix it entirely on my own. Once it came back, I replaced the recoil spring with a 14-lb. Wolff spring and then fired 345 of the same three ammunition types (Norma 124-gr. FMJ, Speer 147-gr. FMJ FP, and Federal 147-gr. HST) without a single malfunction.
3. The magazines seem fine - I invested in a pair of matching Staccato 17- and 20-round magazines in case it was bad magazines. There was some suspicion about the Duratech OEM magazines perhaps not being good quality, and some people indeed have had issues with them. However, after replacing the recoil spring, all four magazines fed perfectly. The Staccato mags feel nicer and rattle less than the Duratechs, but the Duratechs fit the gun a little better.
On some additional shooting, it continues to be an extremely ergonomic, pleasant, mild-recoiling shooter that is quite accurate. Only two new-ish observations are that it seems to shoot fairly high, which may just be normal because I was shooting at IDPA targets at 25 yards and not for tiny groups at 10 yards. I'm not an amazing shot, but in a hundred or so rounds at 25 yards, I only dropped maybe 15 points on the IDPA target, and none outside the -1 border. At 10-20 yards, it will shoot out the black of any target I had.
The other new-ish observation is that the gun shoots differently with the 20-round magazines. Can't really describe it, it's not really milder, but it does seem to come back on target a little faster.
The extractor is also not great and it really needs replacement and tuning. I think the recoil spring fix, while making the reliability much improved, also changed the cycling rate enough that the ejection is weaker and it's getting perilously close to brass-to-face.
Truthfully, if you're looking at getting into 2011s, you can do worse. It's a great entry-level gun, and therere are a couple features on it that are honestly nicer than Staccato. The grip is much nicer than the Gen 2 Staccato grip and on par with their Gen 3 Tac grip. It's an attractive gun. And while it's bobbling out of the box for a lot of people, switching from a 9- to a 12-pound recoil spring in the 5" model and from a 12- to a 14-pound recoil spring in the Commander seem to resolve problems for most people. That being said, if you're thinking of getting into 2011s... saving a bit more for a Staccato is also not a bad decision.