Probably because Chain of Memories itself is a port and wasn't made just for the HD ReMixes but instead it was originally remade as part of Kingdom Hearts II Final Mix+ when that released in Japan.
When they decided to release the ReMixes they didn't want to postpone any releases of them, so they just took the already made cutscenes for Days and combined 'em into a movie since they were prerendered so no extra work there. Sure they did a bit of extra work for the Re:coded movie in 2.5 but it was still minimal overall, they didn't want to postpone anything to remake entire unique gameplay systems which Days and Re:coded have in comparison to the other games. Even by their standards, the remake of Chain of Memories is minimal since all it really does is add a couple new things and make the world 3D by reusing an existing engine. And again, CoM was remade several years before the ReMixes were even considered.