Mmmmmm.... yes and no.
The movie begins and ends during the timeframe of WWE. However, in the in-between time you go quite a bit farther back. If jms himself thinks it's fine to watch it first, that will probably hold true for a great many otehr folks. I'd still disagree with them.
Well, for anyone not really familiar with what the episode titles mean...
"In the Beginning" is set roughly... 18 years?... after the final "regular" episode of Babylon 5. But it's a narrative, and most of the events being discussed are set about 10 years prior to "The Gathering" (the pilot movie).
The very final episode of B5, "Sleeping in Light," is set 20 years after the final "regular" episode of the series.
SO... if you're like me and prefer to watch things in the "in-fiction" chronological order, that's why I recommend "Sleeping in Light" as the last thing you watch.