Object based audio won't do anything for stereo/5.1 mixes. If a sound utility is doing something to a stereo YouTube movie, it's something instead of object audio mixdown, which it shouldn't be doing. That's akin to having an amp advertised as being an EQ, but also adding reverb - you want the reverb to be a separate component or feature so you can control it. There are plenty of audio 3D space enhancers out there, so there's no real need for any to be integrated into Dolby Atmos.
From your linked description, Atmos doesn't claim to enhance stereo audio and doesn't list YouTube as a source for Atmos enabled audio.
Dolby Atmos receivers typically (if not universally) can do upmixing via "Dolby Surround" of non-object based tracks to derive height information. As a superset of Dolby Pro Logic IIz, Dolby Surround can upmix even stereo sources to output in full Atmos. I have no idea, however, if this is implemented in Dolby's software-based decoders/mixers.
There's a pretty good write-up here. It also contains impressions from an a/b comparison between a stereo downmix upmixed back to surround by Dolby Surround vs the original multichannel mix and some test files if you want to do your own evaluation.