This is done by the wysiwyg editor. (the oembed plug-in does this). The reason is that you cannot use a http:\\ link on a https website. The browser will complain about insecure content.
The solution is to use // in stead of specifyon http or https explicitly, and the browser will automatically chooese the same protocol as the page it's loading.
Now, this doesn't work for file://, hence it doesn't work for off-line exports.
I can see 2 options:
1. Embed the youtube page without using the oEmbed plugin (but go to source mode and enter the required html yourself.
2. Edit the exported offline_template.js file after export.