> But there's a third issue: websites can easily determine whether you have allowed JavaScript for them, and if you disable JavaScript by default but then allow a few websites to run scripts (the way most people use NoScript), then your choice of whitelisted websites acts as a sort of cookie that makes you recognizable (and distinguishable), thus harming your anonymity.

How would this work exactly? And if it did work, wouldn't it at the very worst only work on sites for which you had enabled JS? I.e. sites that you had already essentially conceded your anonymity on by choice?

I don't see this as a worthy argument for enabling JS by default and destroying users' anonymity without custom configuration.