I may be wrong, but I seem to remember that while in the tutorial region, you were restricted to only the most basic harvesting actions -- you can upgrade the quality stanzas, but not the rate or speed, nor the type (gentle instead of harmful).Whether this is intended, or just an old bug dressed as a "feature", I do not know. But it seems to be by design, just like ranged weapons are not available in Silan.So, those actions are grayed out for now, even though you fulfill the prerequisites.
Yoh Yawh (the Harvester Trainer on Silan) does not offer any Speed or Rate stanzas for training.
"Harmful Extraction with Rate 1.0" is a bit of a misnomer. IF you right click on that action, you will see it has the prerequisite stanza Rate 1.0 (which you noted correctly that comes with your character), but what it contains is the stanza Rate 2.0. So, when you'll be able to buy it, you'll buy an upgrade for your rate: https://imgur.com/a/6Nbkium
Isn't "Harmful Extraction with Rate 1.0" the same as "Rate 1 - Harmfull" - the prerequiste for a stanza is the stanza itself? This shouldn't be listed since the Rate 1 stanza is automatic.
My home is always sweet Yrkanis..