As requested by @juliushaertl (nextcloud/server#7441 (comment)) I've created this issue.
Expected behavior
Depending on the selected theme color the notification alert color, and maybe others, should automatically be adjusted to be still visible.
Current behavior
No automatic color adjustments seems to take place at all.
Steps to reproduce
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Open the admin settings.
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Change the theming color to FF0000.

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Check the notification symbol in the menu bar

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The notification alert is nearly invisible.
Better visibility could look like this:

Environment
Server Configuration
OS: Linux 3.16.50
Web server: Apache2 2.4.29
Database: MariaDB 10.0.32
PHP version: 5.6.29
Nextcloud version: 12.0.4
Client Configuration
Browser: Mozilla Firefox 57.0.2
Operating system: Windows 7