Egypt is not 'non-favored'. The US has very close ties with Egypt's dictatorial regime[0], despite its awful domestic human rights record[1].
[0]https://thehill.com/blogs/congress-blog/foreign-policy/58552...
[1]https://www.amnesty.org/en/latest/news/2022/09/egypt-human-r...
The WTO sets the MFN list and Egypt isn't on it so strictly speaking you aren't correct.
Besides incurring WTO favor, the US also bestows it's own preferential treatments to those same nations. Egypt has long received many of those preferences so you're right in the ways that are most relevant.
That said, I wouldn't place Egypt on US's BFFs! Top partners in crime list - the one that includes 5/8 eyes nations and Israel.