If my memory serves me correctly, ANer M909 took/ is taking the Bachelor of Commerce/ Master of Engineering pathway at UoM. If they're willing, perhaps you could talk to them. I'm pretty sure that some other ANers are taking the Bachelor of Science or Design/ Master of Engineering route at UoM, who you might be able to talk to. They might be able to answer the questions you have above.
In your case, I'd probably talk to UoM first and see what they say about your questions above. Pretty sure that you can take one of the pathways listed
here (see the first set of dot points), which appears to imply that you can get into any major in the Master of Engineering via the Bachelor of Commerce, as long as you do the designated subjects as breadths, but I would get that confirmed as I'm not 100% sure (someone else may know though). Also, check the expiry date of the scholarship offer. If it's closing soon (e.g. next few days), check the conditions and accept if the scholarship conditions say that you must be doing the Bachelor of Commerce degree to receive it (which is usually the case). Then, probably would put the Bachelor of Commerce as a preference, but not the first preference, if you won't be able to do civil eng in the Masters without the civil systems major in the Bachelors. If you wanted to study the Bachelor of Science or Design more than Commerce, do the same. If Commerce has now become your most desired course (regardless of scholarship), then put that as your top preference.