The score keeps time with the recording, intro and ending included
When you practise with a song's recording, a tab's count-in or intro that the recording doesn't have no longer throws the first bars off, and the score follows the drummer more closely through the whole song.
When you add a song's recording to a score, the player works out where each beat of the score falls in it, so the cursor and the click follow the band. Three things could throw that off, and all three are fixed.
Bars the recording doesn't have
Tabs often open with a count-in, or an intro from a live version, that the album recording doesn't play. The player used to squeeze those bars into the recording's first seconds, so the first few bars went far too fast and the click lurched from one bar to the next. In Waking the Demon, for one, the first ten bars swung from 128 to 237 bpm and back. Now bars like these are left before the recording starts, at the band's tempo, and the song lines up from its very first bar: those ten bars all play at the band's 128 bpm. The same goes for a tab that runs on after the recording ends.
Following the drummer
The player used to listen for the notes in the whole recording at once. In loud, distorted songs the wall of guitars blurs the drums, so in places the score sat a little off the band, most of all where a band that doesn't play to a click speeds up or slows down. Now the drum part of the tab is lined up with the drums alone, taken from the recording's own drum track, and the beats land on the drummer's hits more often and more exactly.
Long riffs and endings
In a riff that repeats for many bars, the score could drift a bar or two late and still seem to fit, which showed at the end of a song: the end of Laid to Rest came in about four seconds after the band. The player now also listens for where the drummer stops and starts, so it keeps count through most of those riffs, and that ending lands with the band.
Scores you've already added a recording to are lined up again the next time you open them, which takes a few seconds once. A tab that has a bar more or less than the band plays in the middle of the song still can't be lined up there.