Well NIS made the game. They have access to the source code and original programmers. They can make alterations to the game engine, because they actually made the game. Same goes for Nintendo, Konami, Capcom, etc.
Groups like Natsume only license the game and a few of the development tools. That doesn’t give you access to the source code; nor does it give Natsume permission to alter the game engine itself. Natsume has talented programmers on their payroll, but they don’t programmers that talented. Of course they could hire some, but that’s not the kind of money they have, else they’d make their own games from time to time.
Atlus had a REALLY sweet deal when they worked with NIS. They got a lot of favors from the original Japanese studio, most game companies would kill to have. Same with Working Designs, when they were popular back in the day. Not all companies are created equal.
There are a number of reasons for that. Just two off the top of my head:
#1: Methodology of voice storage. Different studios have different ways of handing audio files. Therefore how the audio is stored widely varies. For some titles it’s easy to include additional audio files (and thus have English and Japanese). For others the method makes it impossible to “add” more sound to the engine: especially games that combine the sounds in a single file. Overwriting the original file is easier than appending to it. For some games the size of certain files has to be a specific number or the engine won’t start them; that makes dubbing difficult and so it’s not considered.
#2: Licensing costs. There are quite a few games, where having the original VA’s means paying the original VA’s more money. I know of quite a few games that were meant to have dual language, yet had that feature pulled when such a fact became known. I know of titles that were outright canceled in the negotiation phase because of this.