Braga's "aternate timeline" excuse for Enterprise came about after the second season when too many continuity errors were stacking up, so he used this to try and wipe the slate clean and explain the recent Borg episode Regeneration. Also, some believe it was also an attempt at creating drama for the Xindi storyline in the coming third season by making the audience believe "anything could happen." I doubt it was the original intention that Enterprise was supposed to be an alternate timeline, and certainly by the time Manny Coto took over in the fourth it became very clear that he considered it the same timeline as the other shows.
Besides, if Enterprise were an alternate timeline, than TATV (a Braga co-written episode) wouldn't have been possible, and if the Borg's presence in the 21st century had any impact on the timeline, there should have been a noticeable difference in the DS9 and Voyager episodes which aired after First Contact's theatrical release.