What you want to do sounds like it's very much in line with the uni courses you're tossing up between. I'll start off by saying that it's definitely going to come down to much more than just your university when it comes to getting a job, it's moreso what you've got yourself involved in, what groups you've joined, what work experience etc, so in the end going to either one will not harm you.
I personally chose Monash over Melbourne because their system is already well established, you can do honours without having to do an extra year, it was more convenient for me, and the extra-curricular activites at Monash really appeal to me. The masters at Melbourne isn't really a Masters in my opinion, you do the same, if not less subjects than a Bachelor of Monash, and employers are going to be smart enough to realize this as soon as the uni starts churning out these graduates. The Masters takes what I think is a 65% average, which isn't too hard, but will require some work, and it is possible that you could slip below.
The prestige of Melbourne University in my opinion will not help you that much, and has nothing to do with your Gender. There are plenty of programs and additional opportunities that they give to girls in engineering, and I think you shouldn't be too worried about it. You'll find yourself surrounded by guys no matter which uni you go to if you do engineering subjects, but hey, that's not necessarily a bad thing is it?

Your commerce subjects will be more even.
In response to your PM, I'm definitely enjoying my double degree at Monash, and definitely do not regret it at all. The workload is manageable, you seriously don't need to put in anywhere near as much as you would have in high scool for a 94, as long as you can learn effectively.
Either way you're not going to be making a mistake by giong to either uni, but from where I stand have no regrets choosing Monash over Melbourne
