Some FLAC encoders have a quality setting. But that should not affect the quality of the data in the file. It generally affects the amount of processing time / memory that the encoder is allowed to use. More time and effort gives slightly (like a few percent) smaller files. The decoded output in all cases should be identical to the original. The decoder algorithm on the Phatbox should handle all flac files correctly and gve the same results regardless of the encoder used.
Just to be clear for the readers:
The FLAC standard is asymmetrically weighted to favor decoding speed. What that means is that (for the most part) no matter what compression ratio the file was encoded under, the “horsepower” for decoding should be about the same.
There are some great websites out there that talk about the compression ratio vs time to compress with recommendations but I just use the highest flac compression available because even on my relatively old PC, each song only takes a few seconds to compress. Since I use paranoid settings on my ripper, it sometimes takes hours to rip a CD. Spending a few extra seconds compressing the files as much as possible doesn't seem like a big deal.