Color is preference. Seems each time Duci updates TMO he'll post SS of his color changes for debate and basically go with a group opinion. I think sometimes it's not so much one look is better, but people see something different and it looks better at the moment.
I think caustic has a version of his "improved stock env." for TMO....you could check. Not to mention replacing with the stock scene dat and env files would effect TMO's sensors and adjustments. You could just pull just the env. files, but some settings in env. do effect sensors, mostly anything that adjust light.
It's not so much changing scene dat or env file will mess up your game or even sensors, just that he tweaks them for certain sensor ranges, you adjust certain values, it could have much impact of his view of what sensor ranges should be. When I say sensors, that's sonar, radar and visuals. Any changes you make could effect either or all 3.
Many of us make our own envs. I also prefer a more neutral ambiance that the blue of TMO. You can see what many of us do in the Screenshot thread. If you want to change water colors, just copy the scene dat and Env. files from TMO into a file, make a mod. All you need out of the Env. files is the Env. atl.dat. Unless you want to do a lot of testing, the only thing I would change in scene dat is the light and dark water colors, although they're are several files you can adjust without effecting the sensors of TMO. When you open the Env.atl dat you basically see 3 weather types, each with numerous values based on time of day/sun angle. You could change the waterlight and waterdark colors to progress as the you like during the day. Just know several other values must be considered that effect water color, clouds, sun brightness, ambiance, etc...
If you need help, you can PM me.
Edit:
Here is caustics ISE mod for TMO
http://www.subsim.com/radioroom/show...=194657&page=7