Default ship designs buggy?

Are the default ship designs buggy or special? What I mean is that the default TAS colony ship shows two colonizing modules, but can only take on 500 colonists, not the expected 1000. If I remove one of those modules, there is no resulting decrement in space usage. This goes for some, but not all, of the other modules that are on this and other default ships. They do not take up space or cost, but they also do not provide their benefit.
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The appearances of the core ships are independent of the actual components on them, so there are a number of cases like this. There are mods such as my own KHSM which allow you this ability in your own designs.