I think this is the case because you can warp to a base that doesn’t have a teleporter, though they really should add a check to see if you have a teleporter and then have that overwrite the base computer as the spawn coordinates.
Why else would you only be allowed one Teleporter per base if its the base computer you spawn at? I’ve a strange feeling it’s supposed to work that way but it just isn’t for some reason.
There is a way to build more than one teleporter at a base though, other players in your party can also build one too however only the base owner can use even the ones other people build. Kind of a silly restriction the more you poke at it.