Things like the look of the Marza have been changed and weapon hardpoints to accomodate their effects differently. I don't believe any actual balance or stat changes have been made, but Moguta and Bailknight will know for sure.
Regardless, since mods with a different checksum can't be played online except for with others running the same mod and version, I always create a copy of the mod and remove the GameInfo and Mesh folders from it.
You can then disable the first and enable that one to have most of the effects work and be able to use it online. I only mention this because you can do the same thing for SP and have no concern at all that anything other than graphical effects have been touched in any version.