You can have it "both ways" if you want, but it quickly becomes very muddy - defer to the OS, but override the deferral in some cases.
Certificate management is fifty kinds of all messed up - and in THEORY everything is designed perfectly and properly, in practice it's all bandaids on bandaids that nobody cares about as long as "things mostly work".
If you look at the FULL design, it's actually pretty good - things like https://en.wikipedia.org/wiki/Certificate_revocation_list CLRs have actual thought behind it - but I know of no system that actually IMPLEMENTS everything, for various practical reasons.
So from a spherical cow perspective, it's well-designed; from a "this has to work in the real world with real things and people" it's ... workable by violation of the design all the time.
I would argue for anything security - if there is a difference between how it works in theory vs in practice - then the theory is flawed. Physics gets to have theory/practice distinctions, but engineering doesn't because the bridge can't fall down.
Trust relationships are fundamental even in the most abstract view of the Web PKI and without the band-aids of Certificate Transparency etc. that trust relationship is: Some random commercial entities that are completely independent of the DNS, make fully trusted statements about the validity of DNS record ownership. It's bonkers to the core. If someone would design it from scratch, of course the domain registrars would be the ones issuing the certificates via their established relationship to the customers, and they would only be able to issue them for the domains they are responsible for. And no: DNSSec does not solve the same problem and is a tragedy all of its own.
Certificate management is fifty kinds of all messed up - and in THEORY everything is designed perfectly and properly, in practice it's all bandaids on bandaids that nobody cares about as long as "things mostly work".