VM-based architectures are really common in the obfuscation space, which is why you have executable packers[1], JS packers[2] and bot management products[3][4] leveraging similar techniques.
As for why the obfuscation is needed: bot management products suffer from a fundamental weakness in that ultimately, all of them simply collect static data from the environment, therefore it would make much more sense to make the steps involved as difficult to reverse engineer as possible. Once that is done, all you need to do is slightly change the schematics of your script every few weeks and publish a new bundle, and you've got yourself a pretty unsubvertible* protection scheme.
Regarding the "trojan horse", I think someone is yet to show proof that it's a Javascript exploit.
(*Unsubvertible is obviously relative, but raising the cost the attack, from say, $0.01/1000 requests to $10/1000 requests would massively cut down on abuse.)
[1] https://vmpsoft.com/
[2] https://jscrambler.com/
[3] https://github.com/neuroradiology/InsideReCaptcha
[4] https://www.zenrows.com/blog/bypass-cloudflare#_qEu5MvVdnILJ...