Q:

Apache-Served CA vs Local Root CA - Which Wins?

I currently have two Apache servers running here and here, both use SSL certs signed by StartSSL. Apache SSL configuration below:
  ## SSL directives
  SSLEngine on
  SSLCertificateFile      "/etc/certificates/thor.vikingserv.net/certificate.crt"
  SSLCertificateKeyFile   "/etc/certificates/thor.vikingserv.net/private.key"
  SSLCertificateChainFile "/etc/certificates/intermediate/startssl-class-1.crt"

Both the server certificate and the intermediate certificate are SHA-256, but the CA cert is SHA-256 on my Linux workstation, but SHA-1 on my MacBook.
I could use the SSLCACertificatePath directive within Apache to force the SHA-256 CA cert, but would this override the root certificate distributed with the OS?

A:

No, it wouldn't, because if clients would trust a random root certificate presented to them, the whole point of a trust store would be somewhat moot.
Two notes about your question:

The algorithm used to sign a trust anchor certificate is irrelevant -- the signature itself isn't used during validation.
SSLCACertificatePath wouldn't help you anyway, as that directive is only used when validating client certificates, which is not what you're doing.

