Good questions, good answers.
I’d suggest positioning the bulkheads on the individual pots at or below the lowest water level you want to maintain in the pots. This system will still work if the tubes to the pots are above the water level in your controller, but you are relying on a siphon effect which can be problematic.
It is best to keep all the plumbing (main line and the lines to the pots) downstream of the controller at or below the controller in this extremely low water pressure system.
Since you intend to expand the number of plants your system feeds, I’d also suggest that you use 1/2" pipe between the main reservoir and the controller so that the only 1/4" tubing is from mainline to the pots.
I’ve lost track of how many plants you eventually want your autofiller to service, but the limiting factor is the volume of water it can deliver. Here’s how I’d model it.
Assume that large vegging plants at the peak of their stretch and early flower need as much as a gallon per day in a typical octopot grow.
The flow rate to provide a gallon over 24 hours is 0.09 ounces per minute or about 5.4 ounces per hour. That is what needs to be delivered to each pot.
So at the maximum flow rate your main reservoir needs to deliver a gallon per day for each plant to the controller, onto the mainline and into the tubing for each individual plant.
I’ve lost track of how large you’d like to scale this system, but with a 50 gallon main reservoir supplying two dozen thirsty plants in late veg you’d need to refill your rez every other day.
Your 1/2" mainline would be plenty large enough to supply 24 gallons each day, and the individual 1/4" tubes can easily handle 5 - 6 ounces per hour to the plants.
I may be missing something, but I think those ideas should guide your design.
Hope this is helpful,
-Grouchy