Since the well costs iron sticks, despite being unlocked from the beginning of the game, it can't be built until green science when iron sticks are unlocked.

This is true. Please fix thank you.

check 2.0.4 out

For some strange reason, I have iron-sticks recipe enabled at start in Factorio 2, with or without Space enabled.

Edit: Never mind. I found the problem. One of my local mods forced the circuit-network to be enabled in control.lua for that mod.
-- myTech = player.force.technologies["circuit-network"]
Forcing the circuit-network causes the iron-sticks recipe to be enabled.

This tech has now been moved a long way down the tech tree in Py.

Iron sticks are available immediately in Py, so moving this behind logistic science doesn't make sense for these mods.

Maybe an option to disable the Science, if Py and the 'Iron Stick From Start' mods are enabled, or just a check to see if the "iron-stick" recipe exists?

go and check 2.0.8 out

Thanks for addressing this quickly