It's never been trivial to configure the Mac in terms of things like skinning, but third-party tools to do so have always existed for those who cared enough to look, and today, if you want to install Linux on your Mac, you can. If you want to install Windows on your Intel Mac, you can even do that. Those options were, at best, incredibly niche back in the pre-Intel days (though I remember toying with SuSE Linux for PowerPC in the early 2000s), and nearly nonexistent in the pre-MacOS X days.
So it's definitely not a simple case of "Apple in the '90s was in favor of customization; when Jobs came back, he locked them all down and made them toasters."