I don't think any small "manufacturer" can have the sort of future security that the OP would like. I don't think this is just an Arduino problem.
It's not just an Arduino problem, and it's not just a "small company" problem either.
Any time you use a module-level component, you multiply the risk that that component will disappear completely MANY TIMES over using the basic components. And the basic components are at risk, too. We were designing a wonderful and expensive product based on a pre-release PPC microprocessor from "PA Semi". Did they fail? No, not really. Apple bought them, and their would-be products all disappeared 
Z80s and 8051s are still around, but pity anyone who designed in a Nation Semiconductor "COP8", or a Scenix...
Likewise, the company spent a lot of time and energy trying to figure out whether we should build a "thing" based on "commodity PC hardware" instead of the custom-built hardware we normally used. It was, potentially, a much cheaper solution, and some of our competitors were doing it. Eventually, we decided that "commodity PC hardware" had a product lifetime SO short that all the time we saved not designing our own HW would be spent "vetting" the latest version of the commodities
(I've still got a fair amount of equipment designed to connect to a PC's parallel port. "hey, there will always be PCs, and they'll always have a parallel port!" Oops.)