I don't claim to be a professional in the copyright field, but I do have a few bits of knowledge and experience I've picked up in the last year or so. Allow me to address a couple of your points.
There are a few widely-held copyright myths regarding licensing and remixes.. One is that "remixes given away for free don't need licensing," and similarly, "remixes given away for free don't need to disburse royalties to the copyright holder."
The first one isn't true UNLESS it falls under Fair Use, which remember is a defense, not a right. Fair Use can't stop someone from suing you, and if that happens it's your responsibility to prove you weren't infringing on someone else's copyright. Statutory damages of several thousand dollars. Fair Use is decided on a case-by-case basis, so only a copyright judge is going to be able to decide whether or not something falls under Fair Use.
As for the second myth, copyright law requires a specific number of cents to be paid to the copyright holder for each composition, rather than a percentage of the sale price. The only way around this is to make an agreement with the owner to either waive or lessen the statutory royalty amount.
Does this mean that OCR (or insert other X artist here) could some day be held liable for tens or hundreds of thousands of dollars in due royalty fees? Well, no. But the artists who submit their works to OCR could be, as they are the sole owners of their material. (It's in the Content Policy). Is this likely to happen? With current legislation, no. It would (probably) not be worthwhile for game companies to hunt down artists and hand out lawsuits. However, if new legislation passes that changed things to make it actually worthwhile for large game companies to do so, there's not much really stopping them. We've won the SOPA war for now, thankfully.
Of course, none of us think that what we're doing is actually wrong or worthy of being prosecuted. We assume that game companies don't mind our infringing actions, but only because they haven't sued anyone yet. Yeah, some companies are very open about the remixing community, (looking at you, Capcom), but should we really assume that all companies see releasing unlicensed remixes as acceptable behavior? Remember, when remixes are licensed and paying royalties, the copyright holder is making money. When unlicensed remixes are given away for free, the composer (or other copyright holder) loses out on that royalty money. Most people, (especially companies), don't like missing out on free revenue.
In the case of the Kickstarter, (this is purely my speculation), it probably appeared to SE that OCR was using Kickstarter to "sell" the physical albums without proper licensing and paying royalties (though there may have been plans to do so). This of course reinforces the belief that game companies currently draw the line of morality at the point where money becomes involved. Obviously we won't find out until we see what happens next after their internal discussions, but if I had to make a guess I would say the outcome will be that OCR will make an agreement to pay royalties for all of the physical albums "sold," and possibly even a flat-rate one-time royalty fee to cover all of the free downloads on the site. It's anyone's guess.
This is exactly right, though the worst case scenario could even include statutory damages. Again, I wouldn't put so much faith in the companies not taking an issue to infringing remixes given away for free. It's entirely possible that it's just not worth it to the companies until money becomes involved. Then it would likely make things more worthwhile, or at least easier to prove in court.Just things to think about. I do hope both parties are able to reach a satisfactory mutual agreement.
Of course, it's entirely possible that SE is interested in partnering up with OCR and funding it themselves...