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This is probably a stupid question, but as far as I can tell there's not much difference aside the additional parameters in pkcs12 version.

+2  A: 

From the docs, the output file format differs:

openssl_pkcs12_export() stores x509 ... in a PKCS#12 file format.

openssl_x509_export() stores x509 ... in a PEM encoded format.

Frank Farmer
+3  A: 

More importantly than the formats themselves, the pkcs12 export stores off the private key along with the certificate, whereas the x509 one just stores the certificate.

GregS