I don’t know the situation with Mac Scrivener, but if you’re on Windows–
The Spellcheck dictionary is a different dictionary than the one found at Edit > Writing Tools > Dictionary.
Edit > Writing Tools > Dictionary is the WordNet Dictionary, which L&L probably licenses.
The Spellcheck dictionary is a separate file in Hunspell format. If you like, you can download and install a more robust Spellcheck dictionary then the default provides, instructions here. (That thread is in regards to the v3 beta, but still applies to the production version of v3.)
That doesn’t solve your problem, but now you know about the differences.
Best,
Jim