Seems like this bug was fixed, however, when I build a stock ship and try to exploit the bug the factory/recycler allows me to upgrade the ship while it's being built. Although the text is white or something like that, probably meaning the option to upgrade is disabled?
It doesn't come out as an upgraded one, but I would assume the next one will have the upgrades? Doesn't look like it. After I set the upgrades factory/recycler just kept building stock.
While that particular ship is building you cannot change its config, however you can config the other units and wait for the unit you want to config to finish building.