How do I extract X.509 certificates embedded in executables?
Apple's root certificates are available via Keychain.app in the System keychain. Both expending too much effort, confirm the certificates you are trying to extract truly differ from those in the System keychain.

Be sure to review Apple's published source code for their tools, code signing, and signature verification at https://opensource.apple.com or ask on the Apple cryptography mailing list to chat directly with Apple's security engineers.

Mach-O Maybe?

Assuming the embedded certificates are stored in a data segment of the Mach-O files, see the article Parsing Mach-O files for details about how to access this content.

The open source tool MachOView will probably provide enough insight to judge if the certificate is encoded as a Mach-O segment.