Sebastien, Jony, please add comment if you have any idea from UI/UX perspective.

Changing Chrome notification sgtm.

Will this apply to all message center platforms?

What is the motivation for making this change? Are there studies or data that indicate that this is the right thing to do?

It seems to me that hiding the close button will only make it less obvious to users that they can dismiss it.

Extra UI on hover is not an unusual paradigm. I am not concerned with its discoverability and it aligns with the Android notification paradigm, which will be this. 

The original motivation is aligning with the Android (ARC on ChromeOS, actually) notification.

Mac and Windows 10 notifications have a close button on hover as well. I don't think it is bad.

For Mac only banners (auto dismissible) alerts will have the close button on onhover. Alerts will have it always visible.

In general we've kind of already decided that we will be consistent with the OS not across chrome so in this case ARC notifications could stay as they are.

Out of curiosity, is showing the X all the time in ARC notifications impossible?

It's not impossible, just not desirable. 
M based notifications have the timestamp in the way, N notification when we get there have x and setting on hover as well. Keeping X in cros specific notification only makes them less consistent with the upcoming android ones.

Fukino-san, could you take a look? 

I believe this is working now in 59.0.3041.0 (Official Build) canary