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Well, when it comes to YouTube it may actually be worth upscaling to some extent. I've read people saying the increased bitrate 720p video gets when uploaded more than compensates for, well, the upscaling itself. Not sure how true that is, though.
When I uploaded 480x272 vids recorded from my PSP I actually upscaled them to 360p since I expected them to be treated as 240p by YT, and we all know how wonderful those are, also in terms of audio quality. But I never actually tested it, so it's possible YT would upscale them to 360p on its own.
Outside YouTube though, which isn't really the paragon of quality in any case in the first place, we agree upscaling is doing it wrong.
To answer part of the question though, I'd stay away from 1-pass bitrate mode unless you're really hurting for CPU speed (in which case you'd still be better off using lighter x264 settings with a decent encoding mode), if that's what you're asking. Both CRF and 2-pass ABR are acceptable depending on what you want, CRF being the faster and better of the two unless you absolutely need specific filesizes (which you shouldn't).
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