Hello again!
Most crafting Skills actually don't give anything beyond Lvl 2 because most of the Tier 2 and above crafting materials don't exist yet! The game is relatively recent and I have only really implemented stuff up to Lvl 2 in most Skills, though it is possible to get to max skill level (level 5) and earn a title and a small stat boost.
Forest plants grown on your farm don't give seeds for special plants, those are only found on the wild forest plants. That said, Tomatoes are not implemented yet. Was there some recipe that uses them? I had planned to put Tomatoes in soon and I thought I didn't have any recipes requiring them enabled yet.