I used the option --removemapq0 when I ran Coverage.R, since it seemed reasonable that reads with 0 mapping quality should be removed.  There isn't any non-obvious reason why this is a bad idea, is there?

You'll probably get a significant drop in off-target coverage with removemapq0. There is information in those reads and on-target regions with poor mapping are ignored anyways.

I would recommend following the vignette closely and using the defaults for test runs and then work from there.