Is there any benefit to upgrading the conquest yard to level 3? I don't think I remember seeing anything other than "unlocks expert build," whatever that is, or something like that and I'd rather not have it idle for 10 days for nothing when I could just use that 10 days for some ridiculous U1 upgrade.
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Personally, it isn't something that you need to worry about enough to warrant upgrading the Conquest Yard if you have other things to do.
The regular Shipyard is much more valuable to upgrade as it provides a 15% weight reduction for Legion tech, and comes with the same expert build functionality, but it can be used on any class of ship instead of just Conqueror/Defender/Interceptor class ships.