Yes, this is on purpose. Some URL schemes can effectively execute code on the computer when you click on them, so the links are stripped out if the scheme isn’t whitelisted.
This might not be the best place to ask this, but after changing the JS and recompiling the assets, nothing changes. The old assets are still used and even if I overwrite the old assets with the new ones, Skype links are still accessible. I did check in multiple browsers and made sure that my browser was using the new version of the JS.