Yes, merging two large mods would require a lot of work even with BeyondCompare. But there is no better tool that I know of to accomplish the task. BeyondCompare also has a Folder Compare option by which you can compare ALL the files (one at at time, of course) for the two mods.
Yes, I use BC every day. But the point is that it, like any other compare tool, can't really do much for situations where the files don't share common ancestry. Particularly for something like mod files where you have very structured, repeating markup but the data will be completely different and unrelated between the two, it's not going to give you any useful result. In that sort of scenario, what you really need is to concatenate the two and identify/resolve conflicts based on the data, rather than on position in the file.
would it be possible to make a program specifically designed to do this?