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Solution by Brandon_Hein
To disable all notification popups permanently, do the following:
1.) Open Project > Settings > Desired Capabilities > WebUI > Chrome
2.) Click Add and set:
Name = prefs
Type = Dictionary
3.) Click on the ellipses under the Value column. The Dictionary Property Builder window will appear. Add a new property with:
Name = profile.default_content_setting_values.notifications
Type = Number
Value = 2.0
4.) Click OK, then OK again to apply the settings.