If you are really serious on making this Roman mod. Don't include aliens or zombies.. it dilute the spirit of this mod. They have no place in an ancient historical mod.
As with interception, please read what I wrote prior.
You can have wagons as craft. Filled with soldier,
Please see screenshot 1, this is a pair of vehicle from the 40k mod. You can have a pair of Canvas cover wagons that move at human pace around the Roman World.
If you are going hybrid, the wagon can transform into ships on sea texture like this from the chronicle mod. See screenshot two,you can have roman legion boarding enemy ship with the corvus. You can easily change wagon to ship with mapscript in Aliendeployment.
That means you can only have two type of craft and ufo, Both Craft and Ufos are Wagon on land and Ship in sea. You can limit craft weapon to have pathetic interception and damage absorption but having almost unlimited range. Like For example, a Wagon can be 4 or 5, filled with 80 Legionnaire and Cavalry and the opposing side is another wagon with Barbarian horde.
Bases, you probably need to redo all the maps into a surface base. Like a real Legion fortress with walls and etc.
As for matching Dioxine, you can, if you believe in yourself. God hood is just a Myth.
I will try to make mod somewhat historical, but some mystical and technological elements need to be in it, as there will be no R&D without them, the very core of X-Com. Mid-game should contain some steam engine-based tech, with almost WWI tech in the end. Without at least a dripple of new toys, the game will get monotone very soon.
As for crafts, starting one will be marching camp, slow, and possibly a single scorpion/balista/onager can be there as well. For interception, I will be relying on Hunter-Killer script, so aliens will attack you. You will get faster, but unarmed and more expensive horse option soon after. After that, steam zeppelin. I know you don't want ahistorical stuff, but then again, I cant make X-Com mod without research, development and interception.
Bases wise, yes, I will probably need open sky, but I will not be focusing on that in the first version.
Just keep in mind, you cant have a whole legion in X-com. And especially not in a single battle. 20 soldiers is crowded as it is.