@rijul: please find my IMHO suggestions below
Yes, both flags should be set on for Items that are operated by both companies.
There is a way to set up this per company. Every warehouse can be attached to a company.
This can be set up for every company separately.
Quality inspections are set up per Item (rather the per a Warehouse). You may want to review Incoming and In-Process Inspection for more insights
It is currently configured per an Item … (not per Item/Company combination)
Please also review the useful articles/forum threads below