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It addresses different bioinformatic use cases, but plink2 is an open-source tool that is widely used and makes extensive use of zstd. In particular, it accepts both gzip- and zstd-compressed text files as input, but output commands that can generate large text files often only have a zstd compression option.

For those toolmakers they would probably say something like "our tool supports uncompressed data specifically so you can add whatever compression you want in your pipeline for your use cases."

Yes exactly. If the most common tools supported zstd then it would make it easier to store zstd FASTQ. At the moment I believe almost none of them do.