1. Most stuff, I've added some of the old FS1 and FS2 non combatants for civilian/merc mod makers to use, I don't think you'd see the Chronos on the front lines anymore
(The Chronos is there for those who want to use it, and I quite like it)
2. You can run both at the same time quite easily, but I'll be using the modular tables system to add those. No-one should be adding to the main ships.tbl unless it's absolutely necessary and only then by using a copy of it in a -mod directory.
No-one should change anything in the data directory, you'll just break things and have to reinstall if you do. Want to reskin a ship? then copy the model and/or maps into a VP file to be added to our precreated mod folder, then if they want to change back they can simply delete 1 file instead of having a few hundred files to look through.
We recommend all mods use modular tables to add or change things, since it'll require less patching that way. It'll reduce problems like with R1-SAH and make most mods work without breaking our main campaign, since most mods probably won't make changes to our core ships in the tables.
We have enough entries left for the Ancients and many more additional things I'm porting over from other places, plus any additional stuff mod makers want to add themselves.
I might make an FAQ thread for modders to ask questions about making/using Inferno based mods if anyones interested?