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A correction to my own advice above. I said you could turn usage notes and advisory checks on "in the plugin's settings". That is right for calibre and wrong for Sigil.
In calibre, Doitsu's plugin has a real preferences dialog — from the Edit Book toolbar, or Preferences / Plugins / Customize.
In Sigil there is no such thing. A plugin gets no settings screen at all: Manage Plugins shows name, version, author, type, engine and platforms, and nothing else. A plugin can store preferences, but the only way to change them is to edit its JSON file by hand, or to ship a second plugin whose whole job is one checkbox. Neither is something to ask of someone who just wants to validate a book.
So on Sigil the switch is effectively unreachable, and that is worth knowing before anyone goes looking for it. We are thinking about what an editor integration should do about it — a validator that hides half of what it found behind a setting nobody can reach is not much use.
None of this changes the command line, where --advisory stays opt-in for the reason I gave: a script diffing epubveri against epubcheck has to see the same report from both.
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