Look at Movistar ... they came with Three GC contenders. Didn't work out for them at all.
Really, it is easy ... a team has to have one protected rider, but if at some point that rider loses a lot of time and another rider does really well .... the "protected" status can be reassigned. In a lot of cases, early in the race, a different team member might take yellow, but usually once the climbing starts, the team leader wins it or another team takes it.
It doesn't happen often because usually the protected rider will never be allowed to drop back without the rest of the team also dropping back. However .... A.) Sky is focused on winning Grands Tours; B.) Froome is experienced enough to admit when he doesn't have it in his legs; and C.) It wasn't clear early if Froome did have it.
By letting Thomas win a stage, Froome kept his team in control of the race but didn't have to do all the media stuff, which can be exhausting. On another team, another rider might not have been able to let another rider keep the jersey ... but Froome doesn't need a big ego, because he has long palmares, so Froome could be honest and work for the good of the team.
As far as I know, most teams cannot Afford to hire more than one Serious GC contender ... Sky is a bit unusual in that regard, with Wiggins and Froome, and then with Froome and Thomas. Most teams decide to go for GC and if they cannot sustain that, they turn loose the lieutenants to try to win stages. Some teams don't even bother contesting the GC (Quick Step for instance) and just go for stage wins.
Look at what happened with Vincenzo Nibali and Richie Porte. Bahrain Merida had no one even close to being able to take over as a GC contender .... all its other riders spent themselves early in the climbing stages to set up Nibali, which means they gave up too much time. BMC had Tejay Van Garderen who was close enough to the top to contest GC ... but he simply didn't have it in him. BMC had Porte for the GC and Van Avermaet for stage wins and such ....
Only Sky had a powerful enough team that they could keep up on the mountain stages without completely burning out every single support rider ... and by the end, even Sky had to pick one.