> Wouldn't that hamper the operation of package.el next time it is
> invoked in a new Emacs session?
It depends on how the variable is being used, I suppose. There is a function `package-install-selected-packages' that may be used to install packages from this list if it's not empty.
However, many people may choose not to use this functionality as they are used to or prefer other methods (such as use-package, which I find much better). If one doesn't use this function (or `package-autoremove'), then there's no need to save it.
So I don't believe that the persistence of the list is necessary for all users. It could save some time for it to calculate the default, which is why saving it could be somewhat useful in some cases.