The "provide the same directory as both the input and output" recommendation mostly has to do with the clean command. With the igir clean command, anything in the output directory that Igir didn't consider writing will be deleted. Assuming your output directory was already sorted by your chosen DAT, the logic goes like this:

igir copy clean --dat <dat> --input <output> --output <output> will copy nothing but also clean nothing. For every ROM in every DAT, Igir will look for a candidate, and it will find all the existing files in your output directory. Then, when it considers writing files, it will do nothing, because the input and output files are the same exact file path. When cleaning, Igir won't clean files in the output directory that it considered for writing, and because it considered writing every ROM that is already in the output directory (but didn't actually write anything), it won't clean anything.

So then you can add any number of other input directories, but as long as you have your output as your input, it won't clean your existing files.

That was honestly difficult to convey, I'm very open to suggestions on how to phrase that better in the documentation.