... I thought Tom did a pretty good job of describing why he doesn't like the nail knot, Bruce. A full paragraph describing the problems he associates with it over the years. That little bit of line protruding beyond the knot is the culprit.
Conversely, it took him a brief sentence to describe the benefit of the needle knot - which is mainly that the leader feeds directly into the center of the end of the line and then tied in a bit further down the line making for an exceptionally smooth transition. If I were going to tie a mono leader to a fly line, I would opt for the needle knot.
But, alas, I too use furled leaders for most of my fishing ( the exception being large nymphs under an indicator, which is mostly a winter thing around here ) so I don't have to deal with those knots. On lines with built in loops, the loop to loop works great. Where there is no built in loop, I opt for the Castwell Knot which does, admittedly, have a bit of the same problem as the nail knot - a little bit of line protruding from the knot. That is usually knot a problem since my combined furled leader plus tippet usually aren't much longer than my rod, if as long.
The things I most enjoyed about Tom's article are his thoughts on leader length and tippet size. Probably because they are so close to my own ideas on those subjects. My thinking on tippet size probably got a good start down in Idaho Falls when Jimmy at Jimmy's All Seasons Angler explained to me why he wouldn't even carry 7X tippet in his store, and why he discouraged sales of 6X tippet. As it is, about the only thing I use is 4X or larger, regardless of fly size ( from size 20 Griffith Gnat to size 2 FEB salmonfly dry ) except for streamer fishing.
The perceived need for long leaders seems to me to be mostly based on one, or both, of two ideas - keeping the fly line away from the fishies or getting a better drift, especially when fishing smaller flies.
I typically fish 3-5' of tippet off a light colored thread furled leader. That light colored thread furled leader is probably as visible / observable to the fishies as a fly line is. Best I can tell, having such a leader less than 4-5' away from and maybe as close as 1-2' to the fly has virtually no effect on the fishies going after a fly. ( Maybe, to paraphrase Joni's observation above, I'm only getting 23 or 24 instead of 25 !! )
No doubt long leaders and fine tippets are sometimes needed for smaller flies - but my take on it is that the long, fine tippets are needed to compensate for or overcome the effects of having a rather long stiff mono butt and mid section of the leader. That long stiff butt and mid section are going to want to drag or steer the fly, so a long fine tippet is required to minimize that effect to get a decent drift. The benefit of a thread furled leader is that the entire length from butt to tip is more supple than even 5X or 6X leader / tippet material, so there is no dragging or steering effect to overcome.
The net effect is that if the fishies are not bothered by an obviously noticeable but naturally drifting thread furled leader that is not dragging or steering the fly, very short and stout tippets will do the job a lot more effectively. Instead of "playing" fishies almost to death, you can horse them, quickly get them back into the system relatively refreshed, and get back to fishing.
The fish are always right.