It's less obvious though, you need to know what's happening and why. Likely not a problem for somebody writing a lot of JS, but I rarely see similar constructs in PHP code.
That's true, and probably depends on the code base.
I don't know how these patterns develop - it's very common in JS, but somewhat rare in PHP. Maybe it has to do with the average level of the programmer in each? Or jQuery's noConflict() helped it along with everybody starting with (function($) {})(jQuery), thus integrating IIFE into their active repertoire.
I don't remember (and haven't found in quickly searching) PSR saying anything about that, but that could explain a difference in usage, too.
Most PHP codebases simply don't have much use for IIFE's. A well-maintained project will be neatly organized into namespaces and classes, and undefined variables don't automatically become global. Meanwhile, PSR-1 says that a file that defines classes and/or functions should not have any side effect. So you don't have to worry about accidentally interacting with other scopes.
Anonymous functions and classes are being used more and more, but PHP isn't fundamentally event-driven like JS so there's less need to hand them out like candy and nest them several levels deep. Most of the closures I do use on a daily basis are callback functions to things like array_filter() and preg_replace_callback(), not event handlers like every jQuery code ever written.