I noticed 3 things in the 30min version that aren't in the 45min version. I think it's to get the plot moving along quicker.
1. The scene where they all get into the sleigh and assigned jobs to spread presents over Danville is cut from the 30min one. To replace it, one of the elves says "By jingle, these kids can make things fast!, and the other replying "I told you I read their files" as they zoom out on the sleigh flying.
2. In the 45min version, Baljeet says "I don't want to alarm you, but your house is on fire", and Phineas replies "That's not smoke, it's steam!". In the 30min episode, Baljeet says "Look, someone's using your clubhouse!".
3. In the 45min version, Doofenschmirtz breaks the Sal Tuscany CD before calling to find Barneo, and realising A Sal Tuscany spells Santa Claus (with an embarrassing Y left over). In the 30min version, Doofenschmirtz calls to find Barneo, and then looks at the CD case to see the picture is Santa with a black moustache drawn on it.
There's probably more to make it fit without confusing plot holes. There's a plot hole where they've cut Perry picking up Frosty's carrot nose (I don't think they show the carrot at all) so when he walks into the xmas party, there's no reason to explain why he's holding a carrot, and why he looks shocked when Major Monogram eats it. I already saw the clip on
YouTube before it aired, so I knew why it was funny, but my sisters didn't get the joke until right at the end where they show a similar scene happen.