The colors don't always match... what is the blue wire supposed to be for on the Scosche harness?

It appears as though Honda got away from running other electonics through the stock radio in 1999 model year. If you owned a 1998 Civic you'd need a radio relocation kit to keep some features like keyless entry, etc. It looks as though you DO NOT need this with a 2001.

I owned a 1997 Civic without keyless entry. I had to buy a special harness to allow me to hook up an aftermarket headunit and still have the interior light in my roof panel work when I opened the doors.