As posted over on the East Coast Spoiler thread...Over on CBS's Amazing Race site, there is a video that shows Cara and Jaime talking to Phil on the pit stop mat. The video is 1:33 long and there is still no sign of Kisha/Jen at the end of that video.
I'd say it was an absolute minimum of 1:50 or so as the 1:33 video started after Phil has already told the girls they're team number three (adding a few seconds before the 1:33) plus at least a few seconds for C/J to clear out as we didn't see them during K/J's approach to the mat.
So the "literally seconds apart" was totally for dramatic purposes. And it's possible that C/J would still have beaten K/J to the mat even if there was no bathroom break since I don't think it would take more than 2 minutes for Jen to do her business knowing it's a race to the finish. The producers and Phil played it up because it made for great TV.