More than likely the bolt holes MAY be in the same location, but the shape of the 5th gen body is significantly different than the 4th gens (even between 5th Trim levels) and the 4th gen running boards will not mount up properly.
I think I mentioned this in another thread of yours, but the frames are pretty much identical between the 4th & 5th gen 4Runners, but the bodies are completely different.