Unfortunately, with how itch.io works, I ended up paying the full $9 for the update, not the $2 difference it is between versions. Hopefully the developer won't increase the price again and delivers on the final product.
No, I can't just "add $2". Making it a donation doesn't count. The minimum I can spend is $7. So I either spend $7 all at once for most of the game, or $9 and get everything. I can't just spend $7 and add another $2 later.