Like private APIs that can screw with color output, outside of the app. And so on. The security comes from
1. Defining a set of APIs that you're allowed to use
2. Ensuring that you only use those APIs
Sideloading apps skips that important security check.
If a given private API is a security problem (and I agree that altering the screen's gamma settings system-wide may well qualify) then that private API needs to be actually secured, by taking it out of process and gating it on a sandbox entitlement.
The private API check is done to allow Apple the flexibility to change those APIs without potentially breaking a ton of apps and pissing off their users. It does nothing whatsoever for security, unless your threat model is programmers capable of writing malware but incapable of obfuscating function calls.
If you're worried about malware, sideloaded apps still run in the same sandbox that app store apps run in. Apple's review process does not meaningfully impact security, so the sandbox is all that stands between you and malware either way.