When even a single button disappears from where I expect to find it in an application (and reappears somewhere else), that has never resulted in the application feeling more intuitive or easy to use. It has only ever been frustrating in the most literal sense of that word, and only every caused me to start looking into other programs.
A more subtle undermining of the user's trust that their tools will be where they left them on the screen the next time they open the application is arguably more insidious, not less. Both because it is more maddening to the end-user than a full redesign and because the damage of lost trust and user ire is harder to measure than the A/B engagement data until things progress too far for any easy, non-painful remediation.
A/B testing can be helpful as a part of an actual user study on users who are aware of what is happening. But unleashed on an unsuspecting user population out in the real world with real things to do on real deadlines, A/B testing inevitably becomes a harmful dark pattern.