Well first, there is an issue with carts played on current software modded units. There have been several changes in the encryption methods that have rolled out on various firmware updates. The trouble with saving something on a cart played using a Gateway for instance, is that a non modified system will not recognize those saves as valid. From what I've read, this is most likely due to the Gateway modded units actually applying an older encryption that should not be available to be applied to that cart (for instance using the methods rolled out for firmware version 4 on a new title that requires firmware version 6. That cart should not be allowed to be played on version 4 firmware; however, you can bypass that using Gateway. When you stick that cart into a unmodified unit, it is expecting to see the methods used for carts that should be present in version 6. It sees an encryption that shouldn't be there and kicks it out as corrupt. Now this is simplified and even I may have misinterpreted what I read, but that is how I took it.
As for people using unmodified units and game carts, ask Datel why they haven't supported it. I would assume that they are dedicating the greatest amount of resources to accommodate the areas they see gives them more bang for their buck. They already have games that have Powersaves available for them, so it's like you are swapping saves already in a way (that is assuming that they are not taking any rudimentary data that you may have stored on the cart and applying one big save edit.) They have already proven that they can successfully decrypt a save and encrypt it again with all the bells and whistles needed to make the game see the save as valid.
Unfortunately, there is currently no way to form a software method to overcome the AES-MAC, and you are literally relegated to hijacking the system and making it sign what you want it to sign. The only way to do that is through a 3DS mod of some kind and custom made software. The closest that we have to this is the save swapping between Pokemon games on Gateway modded devices. Granted we are not editing it like Pokegen or Datel, but we are carrying out edits bluntly (by just doing straight up trades,) using our 3DS to apply the proper Gateway encryption, and then porting it over to somebody else. The device treats it like it was a cart that was played on a different unit. Now this is no where near as complex as what is being done by Bond697 and Slashmolder. They are doing edits to their save and successfully re-encrypt their altered saves. As we all know, when we get our saves back from Datel, it is not starting up like a cart played on a different device. This just goes to show you how much more control that they have over the encryption using their mods. There isn't any reason that I could see why they couldn't extrapolate that into some sort of save swapping (although I'm not anywhere near a hacker on the level of Bond697, Slashmolder, and Smea. so this is just speculation on my part) After all, I can take my version of a game (card1 and card2,) play it on anybody's 3DS and save, and then bring it back to mine without any difficulty.
The work being done by these guys will definitely shed some light on possible ways to overcome the difficulties of save encryption. We just won't know how much is capable of truly being done until they release more of their findings. Even Kaphotics though has said that a pure software method to do this like in last gen is a long way off. Right now, we are at Datel's mercy.