Obviously no system is completely immune. Linux was, is and will probably keep being order(s) of magnitude more secure than Windows, especially because of the availability of white box peer review.
Nonetheless, and even taking into account the patching system you describe, when (if) the userbase increases well enough, there will be eventually a sufficient number of careless users who will disable automatic updates AND ignore every advise about updating unsecure packages (maybe carrying over a history of doing that in the windows world).
When (if) that number is significant enough, linux viruses may get to a point of being viable and they may appear.
What I think is that, for a security relatively conscious user, linux will remain orders of magnitude more secure than windows and easier to mantain clean.
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