With a 1250, given the bike will be new or a year or two old max, I'd say stick with a dealer service. When you come to sell it on or px, you'll find that potential buyers will likely to very sensitive to having a full dealer service record - and there will be plenty of other bikes to buy that have it. With an older bike, you have a different set of potential buyers, so if you're sure you're going to be keeping the bike for several years, the independent makes better sense.
Either way, as said above, phone them up and give them a call.
When I had my 1200, I found the dealer service costs weren't that bad - perhaps £500 or £600 every 12,000 miles. The independents used to undercut this by about 15%. But the costs came in hard when things went wrong, so when the normal warranty runs out, I'd recommend getting the extended warranty. It's about £400 a year, but can save you shedloads.