is it safe now to use dnf update in the same graphical shell?

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I understand your concern, but that article reads like it was written by somebody more interested in spreading FUD than in giving their readers the facts. I've been running a Fedora system for almost a decade, now, and have always updated it either by opening a terminal or, most often, by using yumex or the newer yumex-dnf and I've never had any of the problems mentioned. Also, I've been a frequent user of this forum (and the informal Fedoraforum) almost as long as I've been using Fedora and I've never even seen any questions that I remember about that kind of problem. Yes, it's safe to update your system from your graphic shell, just as it always has been.