I wouldn't say that it was SPA specifically. I think a lot of the issue is that a11y standards as described by WCAG and Section 508 can sometimes be extremely vague. When you start getting into "exotic" components, say things like carousels or modals, there is often no agreement on how they should be handled in a universal way. Organizations like NNG try to do their best providing research into these areas and there has been discussion about trying to nail down agreed upon standards, but at the current moment it has been hard to gain any kind of consensus.

I recently started my Masters and in my current role we deal with a11y issues on a daily basis due to our public presence. It can get so frustrating that I plan on doing my Masters thesis in this domain.

Hard to say. The tools exist to do it right. We put some work into accessibility for the SPA we publish at work and it passed an audit and I’ve used it enough with a screen reader to be sure it’s OK.