I think multi-language spell checking for more than a few words in a second language is pretty much a low probability use case for most users. So supporting either checking in all languages or check only the main language when checking on the fly is just fine as writing a book in Sigil is rare, but fixing up and specifying needed language attributes is more common. So having secondary spellchecking happen in just the spellchecking dialog seems like the right approach for an epub editor to me.
That is what I tried to explain and ask for back when you started this if you check the messages.
Take care,
Kevin