The initial colony ship is not fully loaded. It has 100, not 500 (one of the colony modules is candy, hence not 1,000).
I see the over limit range components on AI trade ships (form the ship details screen). If your trade ship version is an upgrade of one of those, that would explain it. If you design your trade ship from scratch I believe the stated limit holds.
I noticed the trade ship overage under beta 3A
I noticed the colony candy (and verified it) under beta 4.
I re-design(from scratch, not upgrade) all the core ships. The core designs do not fit well with my tech strategy. (thats my story and I'm sticking to it)
edit: from beta 4. Arcean ship
I tried to duplicate the components from scratch and adding all the components except for the trade module brought the design to 64/68. The trade module is another 30. 94/68? oops. (above trade module on list is transport hull)