Just copy the mp3 files directly to the portable device. Do not transcoded.
Encoding the resulting FLAC as MP4 won't give you a warning, because the encoder will no longer be able to tell there's distortions just from the file format, but the end result will be exactly the same loss of quality as the MP3-MP4 "direct" transcode.
lossy -> FLAC -> lossy only to shut up fb2k warning is a complete non-sense, and actually is worse than simple direct transcoding.Since FLAC only supports integer PCM, the latter process inevitably involves with quantization (with or without dither / noise shape).On the other hand, in case of direct lossy->lossy transcoding fb2k will use float32 as intermediate PCM format as far as encoder supports it. Unnecessary quantization doesn't take place.Although difference may not be audible, you are just making it worse by adding chain of task. Do it simple.
Do it simple.
The question is what DAC technology can handle samples above 0dbFS.