Your interpretation is correct, the items in that allow list on the Threat Protection page are related to the AMP engine, so any sites you explicitly allow there get excluded from malware scanning. But agreed, the items you listed certainly look like you would want them blocked, not allowed. Look up whatever the URLs happen to be. That's for the AMP piece, and the same concept for the IPS basically applies, but it's possible there was something legitimate being blocked which prompted them to put something in the allowed list. Also, just a thought, see if you can go back in the change log, see if or what else was changed around the same time, and also see if you can correlate the changes with anything you might see in a Security Center report if it was within the last couple weeks. You might be able to go back further if there were Security Center email reports configured, as long as you can retrieve those emails.
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