Besides, SSO is a major convenience. Assuming that SSO = large company is a flawed perspective, although, I understand the reasoning you're conveying. I believe, however, that only very small companies (less than four people) can easily avoid SSO, because it is complicated to deal with on/off-boarding employees, SSO helps.
And I agree with OP in most regards, for most services, advanced security controls should be available. I think it is far more likely that most companies segregating their security features are not secure by design, so the functionality they're offering is poorly implemented, and by restricting access they limit the amount of support they need to provide to those features.