First Leak, we'll call it "Bribery", had UWTB of 3:47 and MX of 43sec.

Flac (288MB) has the same length-times of Bribery.

The .m4a files from (i suppose) iTunes releases (call it iJapan) have UWTB of 3:45 and MX of 42 sec.

 

So, are there actually some differences ("not final" version from emi mexico might be true in this case)? Or are them "rip"-dependant?

It depends on the rip i think... usually, the rip is made track-by-track from a unique source, so the software could 'decide' to consider a song over during the 'silence' period. The digital track is instead built in a technical way, so I think there's no special differences between the two versions, just the length...