I'd still keep it in mind. Looks matter a lot (more than they should) in a lot of jobs, especially if your goal is to break out of the technical track and go to management. They may be trying to subtly drop a hint of a way you should be improving yourself.

I just found a nice American made flannel and a Taylor stitch chambray at SA today, and I've seen (and gotten) some very nice Johnston and Murphy shoes from there as well. Most of my shirts are jcrew/banana republic/Brooks brothers, 90% are thrifted. Jeans I usually buy new (and I buy nice raw denim), because they're usually faded to absolute hell and torn to shreds before guys donate them, but I still keep my eye out.