The help page tells us that Skritter has 2300 kanji in the database. Yet, the info for 2 Heisig books in the textbook lists says it contain 3007 characters. Are all these characters in the database? Or are there at (least )707 Heisig characters not in the database.What does it mean if a character is or is not in the database. Will Skritter not recognize those that are not?

The rarer kanji which aren't in the Jōyō list (plus the few extra we have) will show up on vocab pages and such, but when it comes time to write them, they will be skipped over until we assemble their strokes. Meanwhile, it reports Japanese characters that people have tried to practice and were skipped, so that we can make them.

You can still practice their readings and definitions, though.