I have been doing a little digging and I think that part of the problem might be due to the fact that tinymce is written in javascript.
The problems re javascript and tags such as embed being used in the editor may be to do with conflicts with the wysiwyg editor code.
This problem is not unique to Silverstripe. I have looked back at other sites that I have used similar coding on and I remembered one I did on another cms platform. The way I got round it that time was to turn off the wysiwyg editor, edit page in html, save and publish page then turn editor back on. It was a simple process on that cms because you could turn the wysiwyg editor on and off in the admin panel.
There will be a way to do it on silverstripe we just have to keep plugging away.
PS if anyone finds solution please share on here.
Thanks
Paul