Hi Jeff,
We’ve just released a new plugin version (v2.5.0) – now it’s possible to set product notes per variation.
After the update, you need to enable the new “Note per variation” checkbox option (in “WooCommerce > Settings > Product Notes > Private/Public notes > General Options”).
Also, you can optionally show variation product notes on frontend, in each variation’s description – to do that you need to enable the new “Variation description” checkbox option (in “WooCommerce > Settings > Product Notes > Private/Public notes > Frontend Options”).
Please give it a try and let me know what you think.