I know where you're coming from, you can read the complete audio review/testing of the Note 3
here,
On the other hand, you don't really get bit perfect players for Android, even the SOC isn't designed to do that, so there'll always be some loss. But there you'll definitely see (or hear) a clarity improvement when you use higher bit-rate formats.
I'd recommend
PowerAmp over the Samsung stock player, it handles FLAC (804-869 kbps, I think) as well as other high res formats. It's well worth the 5 bucks.
If you really want high res audio, you could invest in a portable amp, though firstly you'd have to get a decent pair of headphones. I'd recommend the
Audio-Technica M50s, they're usually under 200 dollars and well worth the money. I've been using a pair for the past 2 years and they only sound better.