Personally, I like the flat top style "cafe's" have (bars tank and seat all in line more or less) and that's what got me, and a bunch of others, into it. I'd call mine much more in line with that bike in the article on the "gentleman's express" bike on here a while ago (minus the internal engine mods) than a true cafe (imo meaning a track bike for the road). I think the meaning of the movement has been lost in translation largely and that's what creates this huge rift between the cafe crowd.
However, I don't like cutting up originals in good condition and I don't have the skills needed to make a proper handling race bike, so I, and many others I know, stick with exhaust, bars and rear sets to give the look without screwing anything up. Plus, I can put mine back to stock (a look that I'm also fond of) in under an hour and I think that's the way your "custom" should be if you don't have the skills to make a nice piece.
My bet is that if you talked to some of the guys in Britain in the late 50's they'd say that they saw the same types of hack jobs done by young unskilled kids running around then too.