Unity makes no distinction for alternate and primary extension - they are the same. The primary extension's only claim to fame is it's the one that shows up on the profile page and is the default for transfers and MWIs when you use "x" replacement variable there. That's it.
For direct and forwarded calls when we look up the match on which subscriber the call should be routed to or which mailbox we should log into, the database view isolates us from making a distinction on actions to take based on if it's the primary, alternate or user entered alternate extension. To be fair the docs do cover this...
To do what you want we'd have to implement something like device templates (something I'd like to do but is a significant chunk of work). For each extension you enter (primary, alternate, user entered alternate) you can associate them with a template of settings - these would include retries, digit timeouts, prompt/message speed, conversation to use, PW gathering options and probably a few others. In this way if you call from, say, your cell phone it could use a different set of conversation assumptions than if you call from your desk IP phone for instance.
This would be cool but is not on the short term radar since as noted it is a chunk of work. It's on the wish-list, however.
