no, mods are so diverse and unique that there is no mechanical way to merge mods. The only way is by hand, and even that doesn't always work.

I merged goanywhere and Helios and added some of my own stuff to make a "Clan" mod......but it all had to be done by hand....cutting and pasting into an XML script and renumbering all the infocards....was very time consuming and prone to mistakes. If you try to do this....first make notes about every file that has to be changed.....then check them off as you do them, otherwise you WILL screw something up and cause a crash.