getting fuel additive in both tanks?

Here's a thought. Since you have a shared filler tube that will allow fuel to transfer between tanks, and the fuel system is a continuous running loop driven by the engine lift pump, why not reverse the return lines to the opposite tank? As you drive, the return fuel will drain to the other tank and vice-versa with overflow exchanging via the filler tube and thereby mixing the contents as one. I guess it would depend on how high the filler Y is mounted to ensure it cross flowed instead of escaping out the tank vent (if any).

I don't expect that would be a problem; no more than full tanks in a stock system. The return line is always downhill, starting at the fuel filter which is higher than the filler Y.
I don't know how fast the stock return system will circulate fuel back to the secondary tank. But my basic idea is to continuously push fuel from the original tank where the additive is, into the new tank which would then spill back to the original tank via the Y. If you can't get enough flow from the return system, use a cheap electric fuel pump. Draw engine fuel from the stock tank first in order to use additive while the cross-mixing occurs.