There are examples of two alliance members having bases in the same airport.
In The Age of Flight Air Maarten and Thousand wings are members of the same alliance and share hubs
Newark and Los Angeles
airwaysim.com/Game/448/Airline...
This is against game rules (finally found the rules!) and the game should not permit this.
'Two airlines of the same alliance may not be based at the same airport (HQ or additional bases).'
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The only case where this might go through is where a new member joins an alliance and has overlapping bases. This is not checked by the system to keep it simple since it is a very rare case, and something the alliance managers should take care of.
In this particular case the members have been notified and still waiting for their reply.