The UX issue is directly highlighted in their rationale for the change.
Calls to alert(), confirm() and prompt() cannot be polyfilled or safely replaced in the general case because they explicitly block the main thread. That behaviour might not be desirable, but it was the path chosen when the relevant code was written. While some maintained applications will be able to switch to asynchronous alternatives, many older and unmaintained websites - the long tail of the web, will stop working.
Calls to alert(), confirm() and prompt() cannot be polyfilled or safely replaced in the general case because they explicitly block the main thread. That behaviour might not be desirable, but it was the path chosen when the relevant code was written. While some maintained applications will be able to switch to asynchronous alternatives, many older and unmaintained websites - the long tail of the web, will stop working.