yes, it is backwards compatible, as it is a new weaponclass, that if not defined won't be used anyway.

the replaceweapon is still under testing. it seems to be reliable in all situations, but we though the same before we found a few bugs with it.
same applies to the maxbuildablenumber option from the last patch - under some circumstances it can slowdown armada a lot due to some faulty code i have written. that won't be noticable on newer machines and will be fixed in the next version of PP (actually noone reported that yet )

I think one of the more interesting options for this mod could be the ability to use a system similar to FO, where you could set up Avatars at the start of the game to determine which way the fight will go...

I think that is too specific a change, adding features directly from fleetops. What this project really should be doing is making changes that open up a wide variety of modding posibilities. For something like that you might as well just try modding fleetops itself.