This sounds like the training plots might be bugged out / broken? I've been busy playing Cyberpunk / working on FO4 mods, but before that did regularly use training plots and they were fairly useful. Penalties & operating costs seemed a bit too harsh but were still useful. I believe leveling up should allow it to give faster gains and the rate also being faster the lower the SPECIAL stat currently is. Even besides unlocking advanced/high tech, the relevant SPECIAL stat provides a bonus to the plot's output. ie a Martial plot will provide an extra +1 Defense for every point of AGI the assigned settler has, Industrials will produce more, etc.
What changes would be needed in order to make them useful, if they're underpowered?