Well considering the guaranteed entry for BE is 92 and BSc is 85 (and the combined Eng/Sc degree is also 92), depending on whichever is currently your top preference you will certainly get an offer for it from UAC.
But if, say, you get an offer for BE in the first round. If you want to wait for a second round of offers from UAC for the BSc, you'd have to change your preferences and put BSc as your new #1.
Of course, there's also the option of just doing an internal program transfer after two trimesters worth of study. That is, if you enrol for BE, find that you don't want to be there anymore, and decide to go to the BSc later. (After all, you're right in saying that there is a bioinformatics major for both of them, so you can do either or.)
Regarding Chem 1A, I can't speak from experience, but from what I have heard yes Year 11 chem is necessary and sufficient. If you wanna avoid the bridging course route, self learning Year 11 chem is highly recommended - you're not gonna keep up without Year 11 chem, but you'll be fine without Year 12.
According to the handbook entry for the bioinformatics entry in the BSc route, COMP2521 is going to be necessary no matter what. There's no obligation for you to do it in your second trimester or anything (i.e. you can probably delay it a little), but you're gonna have to do it somewhere down the road.
ENGG1000 is usually pretty tragic because there's no guarantee you'll get good team members and you may end up in one of the bad streams if you pick too late. (Basically for that course you pick a stream to do once they open up the spots, but the spots fill up in a matter of minutes.) At this stage, the only good feedback I've heard from with it is from Jamon, and a select few giving me ok feedback.
The 65 WAM to transfer into the BSc is generally easy. So long as you're not one of those people who put little to no effort into uni, it's fine. (Almost everyone who puts effort in gets rewarded with 65+, i.e. credit WAM.)
Should you decide later on you really want to transfer into the BSc with the bioinf major, doing a BE with bioinf major is certainly a good choice as a lot of your courses will get carried over.
Feel free to ask more questions if you need to or if some of the stuff I said was unclear. Was a little hard reading what you said but I had some idea