There are four things you need to keep in mind.
1> Giving a settler unit ANY combat ability, even if it's purely defensive, will prevent that unit from stacking with combat units (as it'd now be considered a combat unit in its own right). This can easily make the unit LESS survivable in the long run.
2> The AI's behavior requires settlers to be escorted. If you're trying to make a unit that doesn't need escorting, then the AI can't adapt well to this change, because it doesn't have a behavior set for unescorted settlers.
3> If you're trying to have multiple concurrent settler units (and not have them form an upgrade chain) then a bunch of things can get screwed up, like the free settler from a certain policy. You can get around this by giving your new unit a resource cost or other requirement, which automatically prevents the AI from seeing it as a "primary" unit.
4> Settler costs are hard-coded. They're either set to a specific value, like a normal unit, or set to a dynamic value calculated by the AI based on the size of the city to be founded and how many free buildings will be given. This latter system is used for the core game's Settlers, and will change drastically depending on your starting era. So you can't make a second settler that costs exactly 100 units more than the original settler unit, because the game doesn't work that way.
I speak about these topics from experience. In my Ascension mod, I'd added the Colony Pod as a settler unit unlocking in the modern age, to be used mainly for games starting in the future eras. It had a combat ability (strength 50), but purely defensive (couldn't attack), had much better mobility than a normal Settler (movement of 3, and all terrain cost 1 MP) and could paradrop. To keep the AI from seeing it as a replacement for the Settler, I gave it a resource cost (1 oil and 1 aluminum). In the end, it actually worked very well, since in those future eras most units had high mobility and so an escort was still needed even for colonists that could defend themselves.
