Agricultural towers with module slots seems to break. If for example picking up a tree normally gives 4 wood, it turns into 1 wood. With productivity, I can get it to give 2 wood, but thats it. Quality seeds don't seem to be useful either, but they do give normal quality wood, although I am sure that is vanilla behavior.

The one part I can answer regarding this, is that quality seeds have no affect on the output regardless of modules being present or not. But enabling the module slots does allow the quality percentage to take effect and sometimes increase from normal to higher qualities. This is standard behavior for the seeds to have no impact on the resulting quality level that is returned.

I will have to look into your report of the returns being changed for tree planting, I only tested with gleba seeds and the return was the standard 40 fruit.