Function guard_missing_from_document_rules 

pub fn guard_missing_from_document_rules(
    selected: &[Box<dyn Rule>],
    document: &[Box<dyn Rule>],
) -> bool

Whether a lossily decoded document needs MD094 added back to its rule set.

MD094 is a guard rather than one of the outer document’s rules: it says why a file rumdl cannot read is left unlinted, and that answer is owed whatever a mode is doing with the document’s own rules. --only-code-block-tools drops the document set entirely, which would otherwise leave a lossily decoded file reporting clean while a binary file in the same invocation reports MD094 - the same question answered two ways, and the silent answer is indistinguishable from a file that is genuinely fine.

selected is the invocation’s resolved selection, the gate detect_binary_for_rules applies to the other flavor. Per-file ignores, inline comments and severity stay with the lint pipeline, which is why the rule is restored to the set rather than reported from here.