Borders are based on influence, a colony or space installation can generate influence (based on various local factors) and that influence has a range and decay (curve) over distance. If two different factions have influence in the same region (border friction) the strongest prevails.
Movement and Path-finding for units respects borders and when traveling will go around other factions borders. There are of course the usual exceptions such as certain treaties or when they are attacking you, etc.
The thing that's different with how Borders are implemented in "H2" is they precisely demarcate territory and we have seamless open space travel/path-finding unlike others. In the games you mention as far as I know the shape and size of borders are visual approximations but have very limited (or non-existent) interaction with actual travel/path-finding which is point-to-point or star-to-star.
In "H1" we actually had the units travel in open-space (tactical view) but it was limited in that we didn't have a seamless map (tactical and strategic), so you couldn't zoom-in/out as they were moving, and the fact that all units moved at the end-of-turn like in MOO/MOO2. Now units move *during* the turn immediately when they receive an order. This makes it so much better in so many ways both visually and gameplay.
For colonization, the rules are that if another faction controls the system or if there are hostiles/threats in the system you cannot colonize until you remove those threats or take control over the system from the other faction. Borders affect movement, relations and influence but they don't dictate where you can and cannot colonize on their own. I think this is the right approach, what do you think?
The terrain and path-finding system is much more complex and robust in H2 so it's going to make a big difference having the different engine modifiers. Traveling through Nebulae, Asteroid fields, etc has a HUGE impact now, and your ships will path around to find the quickest route with their equipped engines.
One of the things we are improving with Weapons and Armor is resistances, weapons now deal a damage (or multiple damage) type(s) and armor resistances will only stop damage of that type (e.g: Physical, Energy, etc). There is a lot more to say about weapons, but that's for another time