Well, i feel that even if that isn't the case, it'd still be the same way with the Brotherhood and their vertibirds.
Even if i didn't side with them in my first playthrough, i probably would in survival just so i would've have to run around everywhere.
I suppose that's somewhat true.
Although you are in danger of being killed while flying in the vertibirds.
Plus, you have to carry signal grenades, which have weight. That could be something you have to compromise while also carrying food/water/ammo.
And the big downside to the vertibirds is that you can't always tell if a location is suitable before throwing the grenade.
And if it isn't, you don't get the grenade back, which is a nuisance.
So, being able to teleport around via the Institute may be quite a bit more useful than BoS vertibirds.