I was thinking about this yesterday. It's always good to have new features, but almost every time there's a stable release, someone (or sometimes everyone) has issues.
This is not a bash against Scirra at all. This is the nature of software development, and for that reason, nearly every piece of software on my PC has settings to request doing an update before it does so. People should be allowed to update their software when it suits them. I'd rather put up with a "there's an update available!" message every time I open Construct than be forced to use versions which could introduce bugs into my development process.
When I click "not now", that should mean "leave me alone until I'm ready to deal with this", and not "okay just do it next time".
And yes, there are workarounds, like using the browser and specifying a url, but that completely defeats the purpose of installing C3 and using it like a traditional application.
The solution would be to not auto-update C3 unless I tell it to by checking a box.