As for a SDR2 LE, maybe they could do a special first run LE for all copies, and then all day 1ers could get the bonuses, while still being able to get it from a local retailer.
I really can't see that happening either. I understand waiting can be frustrating, but the only way a company like NisA is able to bring over games like danganronpa is by reducing costs to nearly as low as possible while still putting out a quality release.
This tends to mean that most stores won't get many copies at all (don't want to many copies or you will flood the market and not be able to make your money back as prices will crash or your money will just rot on shelves) and pretty much all of the special preorder bonuses need to either be through their own store so they can track all of the numbers and print as close to just meeting demand as possible for physical rewards (yes technically they could just have a set number and ship them out to companies, but if you are going to sell 5k of them either way and no more, why bother giving a cut to a company like gamestop when you can keep it all yourself?) or merely stuff like DLC for other retailers as that doesn't cost them extra money.
I would love to live in a world where games like danganronpa were million sellers and were able to be stocked everywhere and the publishing company could throw special editions all over the place like halo or COD does... but sadly that is not this world and thus if you want something special you will have to wait. NisA doesn't even have priority for printing of physical copies and thus often runs getting shipments out to the last minute (and in many previous cases... even a week or two after that >.>)
I suppose Atlus would be a slight counter example, as they include soundtracks with their games. But they rarely do quality LE anymore, and likely have more on hand money than NisA, as well as a number of titles that will sell better than anything NisA can ever hope for. (persona might not sell FF numbers but it's still pretty solid)
The final thing to keep in mind is that the LE nisA puts out are already great fan service. In general they are fairly priced compared to what you get in the normal version (especially for something like Danganronpa which was just $10 more) having a special bonus for non LE first copies really isn't likely to effect sales. 99% of people who are going to buy this game at launch are going to buy it whether or not some bonus item is included, and the last 1% who won't buy it without a bonus item are quite likely to pick it up the first time it's on sale. A first print bonus would be nothing but fan service, and cost them extra money for the release, something that they are unlikely to make back from increased sales due to the bonus.
Anyways I hope I am not to ramblely (I get that way when tired) I can totally get your frustration though, back in the original neptunia days the gamestops by me got the game in like a week before my order arrived from NisA. It was a hard wait, but the nice part is with NisA's LE it's typically worth it.
Anyways I hope to actually join real discussions about this game tomorrow... alas my copy hasn't arrived yet :/