The basics of CAs, trust chains and certificates are pretty easy to understand once you're roughly aware of public key cryptography.
But then you get into the arcane and confusing details of which fields hold which information, the various serialization formats, confusing error messages when servers don't provide their intermediates, other software simply not dealing with intermediates (I'm looking at you, etcd) and on and on.
A "fun" example: I have an openvpn client config that contains, among other things, this here:
<pkcs12>
-----BEGIN CERTIFICATE-----
(base64-looking stuff here)
-----END CERTIFICATE-----
</pkcs12>
This contains, confusingly, not just a certificate but also an encrypted private key.I wanted to change the encryption password, but it turns out that "openssl pkcs12" cannot actually read that block, because it turns out to be a base64-encoded DER format or some other shit. WAT?
Or, oh no, please don't tell me that the PEM block contains PKCS#12?? A PEM CERTIFICATE block is supposed to contain a single DER-encoded certificate.
Everything else is basically smoke and mirrors
Certificate Transparency logs use Merkle Trees so that if they try to hide a certificate, it can be detected.
The system is designed to resist subversion, even by governments. While there are scenarios where a sufficiently-powerful attacker could successfully subvert the system, they run a high risk of being detected if they try. It's just not as simple as you imply.
Kazakhstan had plans to introduce country-wide MITM with certificates signed by a government agency, whose root certificate would have had to be marked as trusted if you wanted to use internet [1].
Many Russian government websites including the largest retail bank had their certificates revoked due to sanctions, which forced the government to start their own untrustworthy certificate center, whose root CA is trusted out of the box by Yandex Browser and has to be trusted if you wanted to access these sites [2].
[1]: https://en.wikipedia.org/wiki/Kazakhstan_man-in-the-middle_a...
[2]: (In Russian) https://www.gosuslugi.ru/tls