I *think* you may be able to submit the spousal OWP app. online IF you don’t send a paper OWP app. in at the same time as the other 2 applications. I submitted all mine altogether (paper), but have just seen people mention the online option when their spouse/ PA didn’t apply for an OWP with their PR apps, and then decided that they wanted to.
And yes, if you are applying inland, the Mississauga office is the place to send everything. I went through Canada Post and paid to have it tracked. Not sure if a courier or more expensive delivery service is worth it. But you should do whatever makes you feel the most comfortable. Good luck!