There are others on this board that know this better than I, but I'll give it a shot. After all, it' been a while since I made a fool of myself, so what the heck.
A skeg will do what it's supposed to as long as it's placed anywhere behind the center of buoyancy on the boat. Without drowning myself into the deep end of hydrodynamics, as a boat moves through water, the bow is inherently more stable than the stern. That makes the stern half of the boat more susceptible to sideways movement than the bow half, which can work to your advantage when trying to maneuver, or to your detriment when the wind is coming in on the quarter. The skeg stabilizes the stern half of the boat, much like having a deeper keel or stern-heavy trim would. A skeg placed at the very end of the stern should provide the same amount or nearly the same amount of lateral stability in flat water as one placed say 2/3rd's of the way back. Then again, as you said, in a boat with a bit of rocker, the stern would tend to come out of the water more in choppy water than the center 1/3rd of the boat, limiting the effectiveness of the end-placement.
Best part about adjustable skegs is they don't add to the windage like most rudders do, though the recessed rudders that were on this page a few days ago actually made me rethink my prejudice against rudders in that respect (nice work guys).

: An interesting idea, but such a skeg would tend to come out of the water in
: following seas and waves--no different than a rudder, but I think part of
: the strength of skegs is their tendency to stay submerged and working in
: seas.

: I vividly recall following my instructor along a piece of coast where we had
: strong wind and tide coming from the port quarter. My ruddered boat was
: continually being turned into the seas and wind, and no amount of leaning,
: sweeping, ruddering could keep me on the line I wanted to follow. I
: basically made it along that stretch by zig zagging, which ate a lot of
: time and put me a long way behind. The instructor, in his skegged boat,
: just paddled along as though there were no quartering weather. At least I
: did not see obvious evidence of corrective strokes and leans as he pulled
: away from me.

: I don't know how much that had to do with a skeg vs my inexperience, but I
: suspect the skeg helped. I will disclaim that by noting that the Eskia I
: was paddling at the time is more subject to weathercocking than the
: Explorer he was paddling. And his 5-star vs. my 3-star "rating"
: at the time probably had a lot to do with it!

: Can anyone elaborate on skegs effect in such situations and on the idea of
: mounting them at the stern?