I honestly don't know which map is right or wrong. If walking between them a lot is proof though, then well, I used to work at 211 Congress St. which requires me to walk past both MT and WT and 20-30 ft looks plausible to me, especially when the increase in elevation is very gradual, so I don't know what else to tell ya.
Here's a more exact way to do it, using the FAA determined starting heights.
Winthrop Square is at a site elevation of 19'. Add 691' and you have 710' above mean sea level to the roof. Note that the 758' is for the original proposal before it was cut, but if you search the archives on this site for 2017 Boston and order it by height you'll see these all correspond to Winthrop. You can also click "determination" and scroll down to see a map.
oeaaa.faa.gov
Millennium Tower sits at a site elevation of 32', but that's from Washington Street, where it rises 677' from the ground, which combined is 709' above mean sea level. These 2 links below will work together to show that the 32' must be from Washington because there's a 24' one that would be from Hawley. These can be found by searching the archives for 2013 Boston.
677' from 32' starting point.
oeaaa.faa.gov
666' from 24' starting point. (note there's also a 648' from 26' so it looks like a 35' total height difference from the highest corner (709' amsl) to the lowest (674' amsl)).
oeaaa.faa.gov
So now what we are looking at is a 710' amsl flat roof for Winthrop vs the 709' amsl top corner for MT.
It also looks like that means it's only a 5' total slope from the bottom corner of MT down to the Winthrop Square Tower, which kind of echoes my earlier sentiment. In short, from the rare angle where these 2 are the exact same distance from you, Winthrop Square will appear just above the top corner of MT. Otherwise it will come down to whichever building is closer is the one that will appear taller in that given view. Hence, why MT looks taller in the pic Stick keeps posting above (it's a block or 2 closer!). On the other hand, Winthrop already looks taller in the stretch run before the tunnel (or on the South Station/90 ramp) when taking 93 North. Overall, Winthrop wins in a photo-finish. (and yes, there will be plenty of photos!)