It is normal for sims to gain skills in gardening when they do gardening jobs like harvesting. The description of this scenario doesn't say they can't gain skills just that it is harder.
The last time I did this my Sim had a huge garden and did not obtain any skills. My current Sim is also now level 3 handiness. It just wasn’t what I expected. I did another one where you are supposed to raise a child from infant to teenager and the scenario ended while the kid was still a child.
Move your Mods folder to the Desktop and delete localthumbcache.package. Then test the game in a new save.
If it works now check for updates to your Mods and CC. Add it back a little at a time while testing until you have found all that are broken.
Thank you for your suggestion but I have never played with mods or cc.
