I think you’re confused about what 3D video actually is.
All of the samples you linked above *ARE NOT* real 3D video. They are called “Anaglyph” 3D.
As with Side-by-Side, Top-and-Bottom, and ALL forms of Anaglyph, it’s actually a SINGLE 2D video stream that is IDENTICAL to any other 2D stream.
If your TV is automatically switching to “3D” mode using active shutter glasses, then your TV must have some form of internal logic which is separating the video into Left & Right images based on the COLOR SEPARATION in the video, and the TV’s YouTube applet must be interpreting the “3D” flag in the YouTube metadata and engaging the 3D mode as a result.
With any HDMI-based video, unless your TV understands that the incoming video is supposed to be DISPLAYED as 3D, you will have to engage that mode manually.
If you were to hook up your PC to your TV and stream those sample YouTube videos to your TV via a web browser, all you’d probably see is a single image with Cyan and Magenta “Shadows.”
3D BluRay is COMPLETELY different. 3D BD has two TOTALLY SEPARATE left & right video streams. They are sent to your TV individually (1080p24 3D videos actually send 48 frames per second; 24 per second of each LEFT and RIGHT images.)
The BD player sends a signal through HDMI control telling the TV the format of the video, and the TV will switch to the appropriate 3D mode.
You CANNOT send full 3D BD images from a BD3D ripped through normal processes via *ANY* media player (there may be one or two on the market that CAN do that now, I don’t know). You will have to use something like DVD Fab 3D Blu-Ray ripping to decode the BD3D stream into a Side-by-Side 3D or something like that.
The YouTube links you showed are NOT side by side. As I said above, they’re all ANAGLYPH.