I'm not counting the Pyramid of Light movie as any sort of canon at all. It was entirely out of character for Yami to want to use the God Cards against any ordinary duelist at all, let alone three at once. It also placed too much focus on the God Cards at all and just made it seem like "the god cards are unbeatable" with it only being Obelisk's ability, but to someone with no background knowledge it was just seem like "oh look, these are the ultimate cards". The way they did it, it is understandable why the movie got such horrible reviews (and as much as I like the series and liked the movie when I first saw it, I can't say I like it anymore). That somewhat dilutes the surprise when he summons all the God Cards during his ceremonial duel with Yugi, and it made more sense there - Marik even mentioned something like "If he uses Ra's ability, he can increase its power to almost 15000!" His goal wasn't to win at any cost, but to test Yugi, which is why he didn't use that ability, or even attempt Obelisk's and just win the duel there and then like he did in the movie.
It's been awhile since I've seen the movie, but I'm pretty sure that Atem didn't want to summon all three God Cards against Kaiba. I think that Kaiba played a card that forced him to summon monsters that had the same level as Slifer did in order to play that Pyramid of Light trap card to remove the God Cards from the game. I also think that the movie had more problems that were far worse than just the way they used the God Cards that contributed to its poor reviews. Though, I agree that it did make sense for Atem to use all three cards against Yugi due to the point of the duel was testing Yugi to see if they were ready to separate, instead of just winning the duel.