I know that Zoiper Pro works with click-to-dial links. However, it seems that not all telephone links in Salesforce are click-to-dial links. Some are, some are not. Those that are not open the native dailer.
I know that some other solutions have apps for Salesforce integration, but I couldn't find one for Zoiper. Dialpad is one such example of an app in Salesforce that replaces the Salesforce dialer with its own.
All of this seems to make sense, and I'm not claiming that you're missing any features or have misstated any features. I'm just asking for confirmation that I'm not missing anything, such as a Zoiper plugin or feature that would make the integration with Salesforce a bit more robust. At the moment, it could be confusing for the end-user since:
a. Zoiper doesn't replace the default dialer in Salesforce
b. All links in Salesforce aren't callto links which sometimes results in the native dialer to be used instead of Zoiper
(At least, that what it looks like.)