I was thinking something along these same lines earlier today. Island Sanctuary would have been great as a place for a FC's headquarters if they could get past the limit of 16 players in the instance. While that's sufficient for the majority of FCs that will never have that many players online at the same time, it would be problematic for the larger FCs that may have 20-50 (or more) online at the same time.
In my experience, FC members hanging out together are usually hanging out outside of the house not in it. They're usually only inside to use the vendors/summoning bell or if the FC is holding some sort of stage event. The island gives players plenty of that outdoor space to mess around.
One of the bluffs overlooking the Hideaway and entry cove would be a perfect spot to locate the FC workshop with airship landing attached and submersible launch below. Imagine being able to see a "life-size" version of the company vessels (even if it's only for looks and not something that can be boarded).
Little customization means little dissatisfaction that decorating in a FC house tends to get reserved to the FC officers.
The island inventory being attached to the island means FC members could share in the gathering/tending duties with everything going to the credit of the FC.
Each FC member could be given their own mammet team(s) at the island workshops to generate seafarer cowries for the vanity items they want. The islander cowries could be a currency system for changing the appearance of the Hideaway in addition to buying things like the glamour prisms/dispellers to share with FC members.