Yep, that's a smart feature. It had actually uncovered bugs in FFmpeg's FLAC encoder multiple times. [1][2] (why they didn't just use the reference implementation is beyond me...)
But I have one nitpick with FLAC in this regard: they chose MD5 as the checksum instead of something sensible like CRC32/CRC64... It makes no sense, because we're not doing cryptography here - we're doing an integrity check. Moreover it makes a parallelized FLAC encoder somewhat problematic to implement, as there's always going to be a serial bottleneck at the end for computing the MD5 hash. CRC on the other hand could easily be parallelized. But I'm afraid we'll have to live with this shortcoming forever now ¯\_(ツ)_/¯