I run security teams for startups with my current firm, Latacora, which is me and 5 other veterans of security firms. Our clients engage with financial services and with regulated environments (like HIPAA/HITECH and the standards and practices of large health networks). Before that, I founded a company called Matasano, which for almost 10 years was one of the largest software security firms in North America. Unlike at Latacora, where our clients are all startups, Matasano's clients ran the gamut from startups to big tech firms to international banks, trading exchanges, utilities, and pharmas.
With the exception of the military, which I on principle won't work with, there's probably no regulatory or audit regime I haven't had experience with.
I say all this as lead-up to a simple assertion: I have never once seen an auditor push back on bearer-token API access. It's the global standard for this problem. If you knew how, for instance, clearing and settlement worked for major exchanges, you'd laugh at the idea that 128 bit random tokens would trip an audit flag.
tl;dr: No.