Possibly, but I think there are some limitations of the DAC chip in the Clip+ (while it does sound very good for it's price, it's not the most technical unit) and I personally have found .flac to be overkill compared to well-encoded higher bitrate .mp3, .aac or .ogg. Just my two cents but you certainly can do some EQ-ing. If the Clip+ has rockbox (that is if you got a new one), you'll have alot of options.
Personally, I can't tell the difference between lossless and Lame encoded V0 mp3. Frankly, I've hard time distinguishing 192kb mp3s from lossless but my hearing is not the greatest either.