I largely agree with you, best tool for the job and whatnot. At the same time, I feel that due to the time I've spent investigating and experimenting with containers, I'm almost better at getting containers to work the way I want than to run it plain.
So if I was now starting a new project solo, I would probably go straight for containers and never deal with conflicting versions or difficult, hacked-together rollbacks, and I don't think it would take me, personally, more time to set up.
In other words, I think it's a good investment of time to spend, say, a full work-week on understanding containers and experimenting on how to make it work for your use-case.