“Not” is not a contrast logic word as “but”, “however”, etc. ( I could be wrong but I don’t think Greg lists it as one of the logic words)
“Not” is a negator that typically functions within ideas.
You are likely not to find/use “not” as the bridge between two ideas like you will typically use “but”, “yet”, etc.
The logic words show the relationship between the ideas, so yes, the “,” is our support here.
Idea 1 \longrightarrow[Du Bois’ foreign trips were the highlight]
Support (,)
Idea 2 \longrightarrow[not the totality of his trips]