Expressing their argument as "don't use custom themes" just makes it less convincing when there aren't really any other easy ways to get the flexibility from them that doesn't cause any of the issues they cite. It would be like finding out that a friend or relative uses the same password for every site, and then trying to get to them to install a package manager by uninstalling Windows and switching to Linux at the same time. Mixing together subjective personal preferences with objective technical advice just dilutes the latter to the point where it's impossible to find it compelling.
The consistency is nice and all, but more than once have I seen distro replace a "stop" button with something they deemed similar enough that didn't make any sense in several applications that used them. I've also seen themes mess with spacing, hiding button rows or stretching them in weird ways. On a glance it all looks nice, but when you're using them applications look weird and broken.
Themes are nice, but unless there's an official theming feature (like with the new Gnome accent colours) it's the duty of a distro to inform their users that theme related UI glitches are the distro's fault, and I have seen none of them bother to communicate that.
Some themes solve real problems, especially for the visually impaired, but that's not the norm. It's a fun work of art, but the utility is always limited. More often than I like to admit, I was left with a broken desktop after attempting to uninstall a theme that didn't work well enough (or at all), and that couldn't be fixed by installing another on top of it.
There are more pressing issues in Gnome than to provide a stable theme API.
This happened together with a GTK UI redesign, turning it into yet another flat UI.