It's a fascinating question Doc. I imagine the reason no one has offered an explanation yet is that we're all equally boggled. I know I am. Still and all, I'll throw my thoughts out there.
First, something incredibly counterintuitive. Jon Lester is actually not embarrassingly bad at holding baserunners. From 2013-2016 (he developed the yips at the beginning of 2013, I as best I can tell) base stealers have been successful against Lester 75% of the time. The league average is about 69%. Of pitchers who have thrown at least 50 innings during that period, that makes him the 77th worst out of 251 pitchers. So he's not good... but there's 76 men who don't have the yips who are worse! Crazy, right? I never would have guessed.
That isn't to say that no one's tried to take advantage. Opponents have attempted a stolen base once every 6.3 innings during that span, good for 78th out of 251 qualified pitchers. So if there's an Invisible Hammer striking down on SB attempts, it's not manifesting strongly in the numbers. This throws cold water on my first theory, which involved Jon Lester sauntering by the opposing dugout pregame and drawling to a pesky rodent coach, "Let your boys know that if I start to feel disrespected when they're on first base, I'll be disrespecting their heads with some high heat the next time they come up." I mean, this is baseball. These guys take the unwritten rules pretty seriously. We're not too terribly far removed from the days of Wade Boggs sharpening his metal cleats. Anyone remember that game a few years back when Felix hit Ichiro, Jeter and A-Rod in the same inning? Broke A-Rod's wrist, nearly ended his career? There may be more than meets the eye, is all I'm saying...
Of course you could argue that maybe without the Hammer, or the threat of the beanball, that SB/IP number would skyrocket to once every couple innings. Still, the fact remains that runners are testing Lester at the 31st percentile, and finding success at the 30th percentile. Both seem pretty darned low to me. So what could be allowing Lester to keep his head above water? Well, maybe it's simpler than we imagine. It's no secret that Lester has dealt with this problem by giving baserunners a loooooooong look before he makes his pitches. The first clip in the Sawchik article shows the result pretty well. The baserunner breaks, Lester glares at him and takes a step off the mound, and the runner scrambles back to first base. I assume he figures that if Lester gets to take 4 jogging steps towards second before lobbing it, those yips might disappear in a hurry. Even if it works, and he throws it away, it's just... I dunno, I guess it just seems kind of brave to take off for second while the pitcher watches you. If it doesn't work, you're going to be thoroughly embarrassed. And pro baseball players HATE that, apparently. That's why fastballs are the coin of the realm, and no one bunts against shifts. I think Lester may be employing this as psychological warfare, even as he struggles with his own troublesome psychology.
Final thought: Lester is well prepared for this kind of staredown-warfare. He spent the aughts with the Red Sox, helping them alternate title runs with the Yanks. Remember those grueling Boston/NY games where every inning featured about 2 minutes between each pitch, thanks to endless pickoff moves and pauses while Kevin Youkilis stood outside the batter's box and glowered at Andy Pettitte? Lester was in the thick of all that. It probably taught him a lot of patience, and the value of the staredown.
That makes me wonder, has Ichiro ever made it to first against Lester since he got the yips? If so, that would be absolutely priceless to watch. Ichiro gliding out to his patented extra-step primary lead, then him and Lester boring into each other's souls until they lose all sense of time and place. I assume it would end with Ichiro swiping second and third while Lester meditated on his own ephemeral existence :-)
Anyway, my numbers all come from here: http://razzball.com/sp-sagnof/
Fun note: at the very top of the SB success leaderboard, you have Ariel Miranda. In 58 innings only one baserunner has attempted to steal off him, and they got thrown out. I expect that poor sod got his Mirdanda rights read to him after his failed theft...