Yes you could have 2 different Jira projects pointing to the same ''Master'' project. It sounds like in your case you would only want create turned on the ''Master'' side for both links, this would also make it less troublesome and easier to manage. Another thing to consider is having stringent poll queries in place on the customer side of the application link so that you only grab the relevant issues from the customers Jira instances, Additionally, if you did decide to have Create turned on for both sides (Customer and Master jira) then you would also need a stringent poll query on the ''Master'' side to make sure that you are only sending relevant information to each customer Jira.