I believe in the past it's been like this to allow airlines to provide branding and allow SLF to know which desks they go to. They also allow multiple flights leaving within a certain amount of time to check in together (i.e. a flight to BCN, a flight to MUC and a flight to FRA, all the same airline, but all leaving within 30 minutes of each other, check in through the same desks).
But with technological advances, you should be able to provide large LCD/OLED/projector screens that display branding, which allows more flexibility as to where the airline is checking in. Dynamic check-in desks for airlines with one or two flights a day could be useful, especially once check-in closes for the only flight in the morning, and another airline adjacent needs more desks. LTN has this kind of flexible arrangement.
I'd venture to guess that it would be more on a capacity/daily basis rather than a flight basis.
S.