There are a couple important carve-outs: 1. The UI is rendered on the GPU now so it’s harder to mess with. 2. A certain amount of customizability is also a security attack surface.
With that out of the way:
MS was already cracking down in the WinXP days. WinXP had a theming engine built in and people made their own themes at first. Within a couple Windows updates they required theme signing, and later the theme engines were removed.
Apple was a little more insidious. Pre-OSX had all sort of interesting opportunities that OSX didn’t bring forward, but even what OSX did have got slowly closed through “api standardization”. System calls getting deprecated one version, disabled or flagged the next. UI paradigms getting thrown out causing applications to be orphaned. Rosetta RIP, etc. On the iOS side customization is functionality impossible as the landscape is openly hostile. Root jailbreak was used for all sorts of fun things as it is the only way to install a modified app or modify the memory of a stock app or add a program that can interact “above” apps and for the people who could do it they went ham even as each window closed and each dev gave up trying to keep up.