The second pop-up is for utilities that change the user's Home tab. Often these utilities hijack New Tab of the browser to insert their own website or redirect the user to another search engine.
Warning when changing Chrome's New Tab page
Warning messages appear in the form of pop-ups that Google added to allow users to quickly reverse the action of the malicious utility. This is important because not all users know how to reverse proxy settings, default tabs on Chrome or even uninstall utilities.
These pop-ups are part of Google's plan to fight Chrome's malicious utilities when they start to appear rampant. Here's an email that Google sends to gadget developers on Chrome in July.
Email Google notifies developers about changing settings via the Settings Overrides API
This email announced that since August 1, the startup, Homepage, search settings or other settings have to be done via the Settings Overrides API. Google added the Settings Overrides API on Chrome to Windows in 2014 and posted it on the Mac earlier this year.