I believe that ESS Tuning, Evolve (UK Based) and Eurocharged make flash units that you can use to swap between sofware tunes (i.e. stock, tune for headers, tune for race gas etc.). I don't know if these manufacturers allow the end user to "self-configure" the software files or not. You may want to give one of them a call though. Hope that helps.
Hey brother I also tune with HP Tuners for GM and SCT for Ford. I asked the same exact question here a few months back but regarding the M6. Same engine and same ECM as your E63 M5. There was a guy named Jim Conforti that had planned to release something called SharkEDT that seemed like it would have been something like what HPT is but unfortunately it fell through a while back. I wish it had not because I would really like to tune my own M6 if and when I pick one up in the next few years. ESS seems like it has something that could end up having the capability to allow a person to self-tune their own M5 or M6 since you have them email you the tunes and load them via their flash-tuning device(think SCT Xcal3 or Diablosport Predator). So all they would really need to do is start offering a version of their software that only allowed the end-user to license and modify their individual vehicle ECM program to develop their own tunes. This is assuming that their flash-tuning box allows for datalogging of course which is a question that I don't believe has been officially answered yet; let alone if it will even read and clear DTC's. I haven't gotten that far with my research yet because I have recently deployed overseas again. If you find anything out let me know and if I find anything out I will make sure to post in here. There are a few of us that are totally willing to do this on here and, understand the possibility of drivetrain damage or even death (TBW settings), and are still willing to sign waivers. Maybe if enough of us keep asking these questions something will be offered.
Great to see another custom tuner in here. Hopefully if enough of us serious DIY'ers show up over here we can really add to the knowledge-pool once we start focusing our efforts towards the Bimmer crowd.
I'll do somemore searching on the tuning. Even a datalogging setup would be nice. Send logs at least for fine tuning. Especially if you can add at least WB logging to it. I'm surprised with so many moded BMW's there is nothing out there for self tuning.
You will need to use some sort of unversal flasher and software. Think CMD, Kess, Galletto. Very expensive unless you buy a Chinese clone which may work or may brick your ECU. The software for these types of units are not easy to navigate like what most hobbyists are used to with Open ECU or even standalones. You will not find all of the tunable tables identified as to what they are; the software can usually identify a "table" within the source code and make it into a 2-d or 3-d graphic but you may not easily know what it is. Any tuner who has identified the tables is unlikely to share that information as it is making them thousands of dollars per tune right now.
You will also want a copy of BMW GT-1 diagnostic software and interface (DSS and SSS I think it is called), you can buy a laptop with the software already on the hard drive and with interface cable... from China.
So yes, doable, gonna be a very extensive project and lots of trial and error. I'd love to collaborate with someone on that, I have some tuning experience but not with this level of equipment, but I do have access to a dyno and am not afraid to fiddle around in the computer.