It means that the mod's maker THINK you could be able to enable/disable it in the middle of a game and continue without issue. But the mod's maker can be wrong (rarely, but it happensJust a small point as to when a mod is "ticked" as not being save game dependant, or something like that, does that mean you should be able to disable it and continue a game without issue...?

Here I think there won't be any problems, but I always suggest to be safe and try it on a duplicated save first.
The problem with loading save is that previous version of R.E.D. (v14, 13, etc..) were not flagged like that and thus can't be loaded with v.15 (and following versions)
Yes, it should not cause issues, but as said, better to do a double save of your current game, so that you can go back from it if needed.If it does mean that then the Xtreme one isn't doing it as I thought that I would disable it to test the difference etc in unit heights and when loaded the game had a faulty corrupted tech tree and no build menus within the city. Putting it back and the game continues fine.