Now that we got our TW3 updated to GOTY edition. Will the achievements become consistent between these two versions?

I've noted that too.

The install for the two games is separate (TW3 plus DLC in GOG.COM directory, TW3 GOTY in GalaxyClient directory). That would immediately restrict access to saves and achievements.

The thing with the PC install, though, is that whether you choose the GOTY or the original line from GOG Galaxy, you end up in the same place with the saves, level and equipment from the original game. The GOTY line in Galaxy does update if you start from there and so does the original if you start from it. Maybe something that GOG could modify so that the two lines become one (and the two installs become one)

I think it is weird that GOG lists them two times.