The thing about codecs is that once the file format and specifications are locked down, subsequent changes are usually pretty esoteric and relate to very specific use cases that most people will never need to care about. For obvious reasons, developers can't make any encoder changes that would make new files incompatible with existing decoders, and they can't make any decoder changes that would prevent them decoding existing files. So it can often be years between any updates of any significance and therefore no good reason to upgrade.
Having said that, this update for FLAC 1.4.0 does sound useful so there could be a case for including it with future releases of MusicBee:
Compression for presets 3 through 8 has improved with only a small decrease in encoding speed, while presets 0, 1 and 2 got faster.
(And if anyone uses lots of different codecs for whatever reason, it might be easier to use FFmpeg instead of the individual encoders and just keep that up to date instead)
Bee excellent to each other...