Include a Disable Auto-Collect game option. Even with a Tile Update Speed of 1000ms, my 13x13 research planet with 5 CBDs can push the webpage to the brink of unresponsiveness. Alternatively, you could make the effect only kick in after you have upgraded it at least once - start at disabled not 5%.
I only encounter the Shipyard bug if I use the new Go button for Fleets. Just conquered two solar systems including shooter battles without any problems.
 "Helixteus II"){kind=icon}
 "Helixteus"){kind=icon}
You can disable auto-collection by disabling tile sync (found in game settings)