I never use the Free ransform or Scale tools. It's faster to use the Selection tool and modifier keys, but that's a matter of personal preference and habit. I disagree vehemently, though, that a file with outlines has broader applicability than a file with live embedded type. 
I can't say I've ever had a problem with overprint preview and anything in ID, but I'm sure our experiences have large areas that don't overlap. I've also been at this long enough to have worked in the days when what you saw on screen was at best an approximation of what you'd get in output, so I rely as much on experience and knowing what my output will be as I do on a screen preview. I suspect that's true for you as well.
I think these little conversations (I hate the to characterize anything that happens here as an argument -- more a discussion of the alternatives among friends) are actually very beneficial to new users. They expose a lot of real-world technique that isn't necessarily covered in manuals and tutorials.
Cheers.