I don’t quite understand this sentence, I’m guessing your output is not quite what you expected to see?
The latest Layout build exports by default in vector or hybrid format, which takes a while to convert all viewports, hence the long wait you experienced as Layout was working in the background.
By unchecking document override you allow it to export raster, which is quick but some elements, particularly transparencies and textures may not translate to pdf perfectly. You could try a jpg or png output and see if you are getting the same. See this thread….