Hey,

If I hand-place quality seeds, they work, also nice work on scaling grow time as well as released spores!
But currently if I put quality seed in an agriculture tower, the script will not trigger the quality replacement.
My current Factorio version is 2.0.69
This bug exists without other mods loaded.

How I got here?
So I was trying out your mod when I started debugging a compatibility issue with mine. (Zen-garden).
Suggestion to remove:
plant_prototype.autoplace = nil in data-upadtes.lua line 32
or replace it with the default
plant_prototype.autoplace = data.raw.plant["tree-plant"].autoplace

defualt value = tree_plant.autoplace =
{
probability_expression = 0,
-- required to show agricultural tower plots
tile_restriction =
{
"grass-1", "grass-2", "grass-3", "grass-4",
"dry-dirt", "dirt-1", "dirt-2", "dirt-3", "dirt-4", "dirt-5", "dirt-6", "dirt-7",
"red-desert-0", "red-desert-1", "red-desert-2", "red-desert-3"
}
}

Might be better to make sure the probability_expression = 0 instead of nilling the whole table.