I have just ran into something and am fairly sure its due to custom tables, when I set a fields admin column to sort it doesn't work using a custom table, but works fine when using the wp_postmeta.
Only thing I can think of is that when it performs the query its using the wrong table.
you are right! The filterable method is applicable to taxonomy and not for meta values. I was wrong to read your documentation. Sorry for the ask. Still, it's an idea.
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