Can't reproduce this. Just checking Code:
#system-message-container joomla-alert.joomla-alert--show {
display: block;
opacity: 1;
}
If I would change opacity to 0, then it's grey.

The opacity is not the real issue. The alert should get a display: none when closed because an opacity just makes it transparent and all buttons behind the alert are blocked. But some clever guys don't see that...

There are some more issues:
#23425
#21803
#25850

This happens on my system. For me it is because I have the windows accessibility setting for reduced motion enabled. The root cause is the stupid fade-in

@ReLater OK, I wanted to see it in grey :-) So, I'm not clever enough.
@brianteeman Think, you mean this here: #25850 (comment)

Yes that's right

I will follow the route as Brian suggests and see what hapens. I am testing
on Windows 10 environment

Pieter

Op 16 november 2019 14:22:10 schreef ChristineWk notifications@github.com:

@ReLater OK, I wanted to see it in grey :-) So, I'm not clever enough.
@brianteeman Think, you mean this here: #25850 (comment)
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Closing as duplicate #25850.