Can any modern company be said to be of similar size to Bell Labs in it's prime? Bell Labs were only possible due to a monopoly supplying massive amounts of funding for about a century. MS had a few decades of domination in the consumer desktop OS space, but they always had competition and I would be very surprised if they had the kind of revenue streams that make this type of long-term investment possible - regular payments from nearly every household and business in the country, with easy ability to make predictions about current and future proceeds just by counting heads.

To be fair, MSFT was not started as a research company and is more of a mass market commercializer of existing technology. Bell Labs' primary goal was to discover new science and invent practical applications. (Reminds me I should go read "The Idea Factory"! (story of bell labs))

IMO new breakthroughs in our understanding of physics would be needed first to make substantial progress in QC. As long as MSFT isn't investing in attosecond lasers or low temperature experiments, RSA will remain secure.