I think I remembered what was bugging me about that whole iOS thing.
It kinda makes sense to me...
So, Apple's Keychain with trusted root CA certificates is available to all apps. When you set trustcerts "smgr", it fails to do that and trusts nothing. It can't import certs into the CA trust store of the device and if it were possible to configure an app to trust any CA undercover/under the hood, then my malicious app just needs to be told to trust Kyle's CA and you get a happy green secure lock trusting an arbitrary authority.
The part I was right about is if you wanted to do mutual TLS authentication from SM to iOS and back from iOS to the SM - that's where you need the PKCS12 with private key, and that's the part iOS won't let any non-Apple app tie into the keychain and get that cert - it must be bundled with the app. Otherwise, malicious app X can use that cert to validate identity, to say, your mail server, and do something nefarious like say, read your email and send it to me.
Avaya's got configurator tools for various clients. Aura Conferencing's Outlook plugin, or Communicator for Lync are examples. You download and run a "installation builder" and it spits out a .exe or .msi you push to your PCs. So, like in the softphones where you punch in server IP etc, Communicator for Lync doesn't let you. Your admin built a .msi where he put in those parameters and what's pushed to the device is the app with all config locked down. I suppose something like that might need to exist for Equinox eventually because you'd need Avaya to sign your app+PKCS12 with their Apple Vendor rubber stamp to get a Equinox version with your specific PKCS12, or they'd need to let you rebuild their app with your PCKS12 and have it signed by you and it'd be something you deploy like any other private enterprise app not on the app store.
I think this is somewhere the whole PKI discussion is going to go more and more. All the stuff I see about it is about how to make the client trust your 3rd party CA that issued the server the cert. I don't really care about that - I'm concerned about protecting the communications core and using certificates on the client that the server must trust before handshaking TLS and allowing a login attempt. Anyone can wireshark a TLS handshake failure and export the CA cert the server offered and trust it to get past that level.