I always design for peak WS elevation for the design storm in cases like this. That way, you've erred on the most conservative side, and you head off endless quibbling back and forth with the reviewer. This tailwater will not increase pipe sized much, and usually doesn't affect any except the final pipe.
I also do a "check" run with the pond full, including design head on the emergency spillway. Not that you have to convey all that flow in the pipes, but it gives an HGL in all inlets. You can then address flood flow relief, if any is evident. I'm sure there is a requirement for safely conveying the 100-yr through the site, even though the design storm is less.