Some Colonies are not being Domed...

Your colonies have no population. Note there is no automatic colonization amount of 1M from the crew as in stock. If you're using the colonize order right away (which will pick up colonists from the planet the ship is constructed at) and instead using the ship to explore first, be sure to transfer some population.

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Space Empires Depot | SE:V Balance Mod

You can also transfer population to the ship before you go exploring as well.

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Space Empires Depot | SE:V Balance Mod

Yes, you'd just use the transfer cargo order to load population.

Any item with cargo space can take population and drop them somewhere else. No additional life support is required.

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Space Empires Depot | SE:V Balance Mod

Watch out when using the Colonize button. If you have added cargo spaces to carry extra population, they will not be filled by the Colonize button, just the capacity of the colony unit. In this case you ALWAYS have to use the cargo transfer function to fully load your ship with extra POP or mines or WPs or whatever.

I load a WP, a spy sat and fill the rest with pop, in that order.

SpaceEmpires.net | Space Empires Wiki

The colonize order will load as much population that can fit on the ship, not just what will fit in the colony module.

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Space Empires Depot | SE:V Balance Mod