Yes this is absolutely the first thing you should do to your car if you have a manual. I wrote a guide on how to do it here:
https://www.supramkv.com/threads/diy-clutch-delay-valve-cdv-removal.18268/
The part number for the replacement slave cylinder is listed there as well if you choose to...
It's not uncommon for BMW clutch pedals. It's usually caused by worn bushings or in this case probably the clutch return spring just needs some grease.
They were admitting that it is a problem at least, just that they don't currently have a fix for it.
I need to set in some other cars to see if I can hear the same thing. It's not extremely noticeable especially before you fix the other rattles present from the factory. I wouldn't be...
Latest update is that Toyota corporate won't approve any more warranty work on this currently because they don't have a fix for it and they're saying that all of them do it. There is currently an open dealer product report (not sure what that means) but as of now there is no fix available from...
Your shift knob isn't loose is it? Some people have had problems with them coming off from not being installed correctly at the factory.
You have to use a decent amount of force to get them to press on. They aren't the screw on type.
Surprisingly replacing the amp did not fix the issue. They're going to try a software update next.
If it's not that it has to be the head unit or wiring I guess.
Edit: No luck on the update. They're waiting for a response from Toyota at the moment.