yes backfiring is acceptable to a point. mine pops nearly every time i upshift or when im engine breaking. the thing is, what is considered "backfiring" to one person is considered nothing more than the exhaust note to others. mine has been doing this since i purchased it, before the crbm, before the full rs5 and even before it was broke in. its just the way the bike runs. if it was a loud pop like a shotgun, that may not be so good, but your little muffled bangs and pops are nothing to be concerned about. and besides that, most motors backfire when running rich, some fuel builds up in the exhaust and when it finally ignites you have your pop. also exhaust valve timing has a lot to do with it.
i highly doubt you would ever need an efi programer for these bikes for recreational riding. hardcore racers may like the advantage of tuning thier quad to its absolute performance peak for each race (different temps, altitudes, humidities and such can change the tune of the car) but for your every day go out and ride it for fun kind of guy, it is really not needed.
personally, i do not race, nor do i plan to in the next year, however i have every intention of using the EMS kit depending on the level of fine tuning that can be done with it (i still have to look into it, waiting for people to use them for a while and work the bugs out) simply because i really dont feel like putting a MegaSquirt system on my r450 to tune for the turbo unless i absolutely have to, although it may make things easier for me in the long run