Good analysis. For the reasons you cite, NYS can't make the Oneida's, for example, collect taxes for the greedy, blood sucking pigs in Albany, on goods sold on the reservation, which is a sovereign nation under both Fed and State law, any more than NYS can force other states to collect sales tax on its behalf. (BTW, when the state requires me as a business owner to collect taxes on its behalf, isn't the state depriving me of a property interest -- my time and labor -- without just compensation?)
Maybe. But there may be a way for you to recover some of that cost. If Labyrinthos Retail is a company that sells products on the retail level and collects sales taxes on the products it sells, you might want to consider creating a subsidiary called Labyrinthos Accounting, Inc. whose sole purpose is to collect and pay these sales taxes. Labyrinthos Retail then pays Labyrinthos Accounting for the time and effort, and deducts the cost of these accounting services on its state and Federal income taxes.
The key, of course, is to make sure that Labyrinthos Accounting, Inc. shows zero profit -- by padding the financial statements with enough bogus -- I mean, legitimate business-related expenses to offset the "accounting fees" it will collect from Labyrinthos Retail every year.