Earlier quoted context omitted.
I expected Messenger would just handle chat messages (ie a direct replacement for my web-based FB chat). That it also would re-route voice calls was not expected, but I don't blame it for that. I do blame it that it doesn't give me the option to disable that functionality. I do not want phone calls to be routed via Messenger ever - yet you have no ability to separate that functionality.
Your friend chose to contact you via Facebook Messenger, for whatever reason. It didn't "reroute" anything. Phone calls are phone calls. If they'd actually rung you instead of using Facebook Messenger, your phone would still have rung.
If you use Messenger to call another Messenger user, it will attempt to make the call as a VOIP call using your data. If you don't have Messenger, it routes it as a normal phone call via your telco 'voice' 3G/4G network. Similar to how iMessage works with SMS on iphones (except with iMessage, I can turn it off on my end)