In my experience all of the civilian XLE ships up to destroyer size (as far as I've gotten, though I mean to change that now that the save issue is better!) are better than the other faction's military counterparts. Its not just the weapons (though they help). They are faster, better armed, better armored, have more flux... the only downside is the fixed forward shields, which is sometimes an issue.
My most powerful ship so far though was a France with 3 alien blasters on it. Their charging sequence will still happen when the fortress shield is up, so you can just flicker the fortress off and back on and still enjoy full DPS. Can't wait till I have some of the bigger fortress shield ships with those onboard. (Have I mentioned how much I love this mod, btw? Easily my favorite.)
iirc the XLE faction's civilian ships are just different loadouts for their military ships.
I agree about the mod, one of the best ones.
Edit: Do you have any tips for fighting the aliens? I get them down to low hull but then they just go phase teleport crazy and end up taking forever to destroy.