It's not the Skype plugin doing that, it's Skype. All the Mitel plugin does is make the calls using the info that Skype has. Skype has no directory of its own, it pulls the info from AD, so this is all about
1/ Having a field in AD that has the 4 digit extension, and
2/ Configuring Skype to use that field to make internal calls, if that's even possible.
Skype is EOL, it is feature-poor, and it doesn't work very well.
For people who insist on using the far inferior Skype client instead of MiCollab, the way I get around what you describe is by capturing the "outbound" internal calls and instead of hairpinning them via the service provider, I route them to a loopback trunk on the controller and use a digit mod to reduce them to just the 4 digits that can be routed properly internally.
http://www.mitelforums.com/articles/3300/how-to-create-loopback-trunk.php