Rhyno,
While there's more than a little good info in your recap of JL's white paper, there's also some misinformation - not sure if it's yours or theirs.
Your description of port behavior may get the spirit of the design's performance more or less right, but it's not exactly correct: Ported enclosures are not merely a "trick" resulting from a port tuning phenomenon. A properly tuned ported box will drive the 3db down frequency lower from any given driver/suspension and will roll off faster below that point than the same system rolls off in a sealed box. That's more extended bass - no trick.
Bear in mind that, as you move lower from the tuning frequency, there will eventually be less bass output from the ported box, due to the more rapid roll-off below the tuning frequency. However, if the port tuning is low enough, as it is on many high-end ported subs (I believe most or all of the SVS subs can be tuned below 25hz, for example), that may not be an issue. For music, the rapid roll-off of a ported sub tuned this way will almost never be an issue.
However, there are definitely other trade-offs with a ported box and I personally do agree that it's much easier to get a good sounding set-up with sealed subwoofers than with ported designs.
As to positioning subs in/near the same plane as the mains, many of the external bass management/digital room correction (DRC) systems will delay the electrical signal to either sub or mains to account for the delta in distance between the sub and mains. This allows more flexibility in optimizing position of both the subs and mains, which may be optimized when they are far from the same plane.
I'm not sure whether JL's own system offers this, but I'm guessing that it doesn't. Since JL's products offer in-sub room correction, it shouldn't surprise that they suggest that it's where DRC belongs (and it also explains their recommendation on room positioning). Personally, I use an external bass management DRC system and enjoy the added placement flexibility.
Running the mains full-range may offer the simplest signal path, but it also eliminates one of IMO the biggest benefits a subwoofer offers. All drivers produce more distortion as frequency drops - the longer driver excursions required for lower frequencies will reduce linearity (increase distortion). The good news is that a high quality sub (like your JL which is among the highest quality IMO) is better equipped to handle the heavy lifting at low frequency than is the woofer in virtually all main speaker systems (even including your Magico, I'd think). If you actively low cut the mains, you remove the heavy lifting from their woofer and shift the burden to the subwoofer, where it belongs. Your mains will benefit from the narrower bandwidth they're being asked to handle. So, there's a trade-off; simplicity vs optimizing bandwidth to driver. Some may prefer the full-range option (I definitely don't), but that's a matter of personal preference not system optimization.
Also, you'd need to consider the room-correction side of the issue. If your DRC is in-sub, I assume that it's functional only to the sub's high cut frequency, yes? If so, and you cross the sub out at 60ish hz, you're only room correcting to that point. In every room that I've ever measured, serious response irregularities run up to 120ish hz and significant irregularities persist above 200hz. Below about 80hz, passive treatments become increasingly cumbersome. If you limit your DRC to 60hz and below, there's a lot of room clean-up that you're foregoing.
At the end of the day, I'd say that most of JL's advice (at least as you've characterized it) is sound, but I'd also note that it's definitely slanted in favor of selling their products.
