Man, you set yourself up for some serious review! Personally, I don't think there's much revoluitonary to what you are doing compared to some of the big players. Lots of them actually bury random code into executables. There may be a minor tweak that I am not familiar enough with your product wrt to online checks, but I beleive that happens already.
However, one concern is the above quote. So, anytime I want to update my exe to have a new set of "over 9000" crypto points, I have to ask you? So, you could become the bottleneck if your product is a runaway success and I can't get your time? Stainless is partly right too. Once a version is hacked, what's the point of redistributing the checkpoints? Only a patched version, that is worth updating to, would be worth re-randomizing checks.
As for the business case for DRM, I think everyone goes to extremes of logic to make their case. Without DRM, you will get a hit on sales, period. Some say every downloader is a potential buyer, others say none. The truth is in between and no one can ever know what that average ratio is. You'd have to release a game DRM-free, wipe collective memories, and redo the release with DRM to know! The point is, unless negligeably low, that is lost sales. It's up to each studio to determine what they think and go accordingly. That's the thrill of business decisions.
I also don't think mild DRM and "Build something good" are mutually exclusive.