Did you think about using the multi-store function of Abantecart? It seems that it might be well designed for your multi-locations. You might need to make an adjustment for a shopper to choose the best location.
But that would allow you to set up inventory tracking by location (great advantage for Store Pickup Items being in stock), you can even set up a different template and ordering parameters for each location, even different pricing if that's applicable in your model - all easily done by a master admin within the default store - or sub-admins at any location or level via users and user groups.
If you've not looked into that as a solution - you might want to see if it would work for you.
Lee