Yes, only one certificate will be created with each domain being in the SAN field. It will be (usually) stored in a directory named after the first domain on the command line.
I believe it will fail completely, as you're asking for a certificate with all those names (and created a CSR with that information).
Switches should override the default ini file. I'm not sure about the order if you specify an ini file using the command.
As far as I am aware, you cannot use multiple webroot paths in the command.
As @Osiris noted, you should use the test server to see what happens. This reduces the load on the production servers and avoids you hitting the rate limits that can prevent you getting a real cert when you're ready.