They are extremely limiting
Assuming you're referring to Fedora Atomic, your statement is extremely exaggerated. Out of the top of my head, the current limitations are iffy akmods and UKI/systemd-boot. The latter of which is being worked on currently and might arrive rather sooner than later. Neither of which I'd assume 95% of Linux users ever engage with anyways...
add multiple complications to otherwise simple tasks
I feel like you don't know what you're talking about. Please be explicit; which tasks are made more complicated on Fedora Atomic?
the padded cell of immutability means you can’t really fuck around and learn how traditional Linux systems work
It's true that you aren't supposed to "fuck" around (most of) /usr during runtime. Furthermore, I agree that the existing ways to circumvent/bypass this leave much to be desired. But, again, most peeps use perfectly fine systems without ever feeling the need to tinker with /usr... And if you absolutely must..., well..., Fedora Atomic doesn't actually stop you. It just wants you to adhere to its ways of achieving it. Making it more of a paradigm shift, rather than outright limiting the user.
If your criticism basically boils down to "I can't make use of my preconceived notion on how Linux works.", then "Yes."; that's exactly the point. Granted, it wouldn't hurt if Fedora Atomic allowed conventional methods to continue working. But as it's currently in the middle of a architectural shift (going from rpm-ostree to bootc), I'd argue they've got more important things to work on.