1. Can the mesh used for the flag be changed?

2.Can vehicles have injured geometries?

3.Can a unit bump into an enemy unit and take over, changing the mesh?(think flood, very unlikely)

And I'm sure NONE of theses have to do with your Halo maps (I noticed all of them do )
1- No it's hardcoded
for the other two I'm not sure
OFF TOPIC
That's Caboose in your avatar right? I love RvB

1, yes, im pretty shure
2. no, they can only have sparks, falmes etc.

Actually I think 1 is possible, I can't seem to find where I thought it said no and the campaigns have many different flags

1) yes it must be possible, Either create a new flag msh and odf or change the existing one's(in the common folder) geometry in the odf to a custom one.

Another question:
Is it possible to have a free-for-all match?

99.9999999999% positive that they had one in some edition of the convo pack, and the v 1.3 patch supports FFA mode (99.99999% sure of this too).