After using the "sign of the times" build for a week or two, I can report that it scores much lower on VirusTotal and doesn't cause alarms at all (at least on my computer)! I have the impression launching builds is slightly slower (I keep my project on an old SD card so file size differences can be felt) but nothing to worry about really. I just have to remember to untick "Remove unused code" every time I start ZGE, otherwise Windows won't let the built programs run.
I agree with Ville that it makes no sense to bloat the file for no reason other than to please security software but it seems there is no other way. The builds are still smaller than anything any other engine would produce for a project of comparable complexity though
btw I see nobody took up my quiz from the previous page

maybe for the best since it's quite irritating (no matter what you do it always asks for a permission, even with a new ZGE build) and when you find out why is it behaving like that… it's unsettling (nothing to do with ZGE).