dotemu version doesn't have this problem. off topic, but annoying music and intro vids can be modded out just by deleting 'adaptivemusic' and 'videos' folders.

manual doesn't seem to mention troop transport. I hope they fixed the mislabeled technologies (armor and countermeasures)

edit: How to do this - build a destroyer, and make sure you build a new one when a hostile navy sinks it, at least that's what the steam version says.

You need to have a ship of destroyer class or higher at the coast of the land you want to go to that is not yours yet and you have no trespassing right. If there are no enemy ship around any more, your troops can land.

1. destroy the enemy fleet
2. park destroyer class or higher at the cost of where you want your troops to go
3. send troops

As soon as the land is annexed, if you choose to do so, you can travel freely within your country from coast to coast.