The blue of the top is a fairly light blue, so it's not that dark. The worst part (for me) is that the pants show a lot of lint. And, it's a pain that the uniform requires 3 different loads of laundry (again, for me -- whites for the coat/socks, colors for the top and darks for the pants. I suppose I shouldn't complain ... I was so overzealous that I took it to the dry cleaners all the time in first semester

). Most people rarely wear the lab coat except for check offs when they are required. Personally, I'm cold all the time, so I've only taken mine off in clinicals a time or two in 3 semesters now.
I bought my own black scrub pants and never had an instructor say anything about them being 'different.' However, there's always that chance ...
And, yes, the tops and the lab coat do need the logos embroidered on them directly, so I don't know of another way to do it.