So I just thought of a solution. The corrosive solution recipe should not use empty containers, but instead output the solution as a fluid. Then, you would need to put the corrosive solution into a container (a recipe that will not accept productivity modules)
Anyway, I'm open to any recommendations and/or ideas.
Honestly, the free containers (except the 3 for 1 deal) aren't a big issue IMO. It's not even close to a closed loop. You can get free containers, but spending far more valuable resources on nuclear fuel. I've found a closed loop for free lead, which is patched, and a barrel-steel-barrel loop which is still in the game, but I'm not using. These ARE balance issues, the containers is just a bit silly.
One of the nuclear mods I played way back when used only fluids, which I'd argue skips the middleman, as there seems little point in filling and emptying containers - barreling and unbarreling machines are a meme, no?
Personally, no strong preference if you leave it, or fix it as you suggest, or remove the containers from the crafting process.