The starbases could both be in the same single sector. If another starbase is in range you then simply add it to the sector and you do this for all starbases that are in range of the first starbase's collection range. Add all the territories they collect from combined into the same sector unless it intersect with another sector, in which case you split that distance.
Preferably the starbase would have a building on them for that though so you wouldn't unintentionally create starbases without planets in them.
Yeah, maybe like a governor seat building or the such that requires trade hub modules and then applies a sector matching their trade reach. That could even open interesting possibilities for variations on the governor seat building type.