Yes, in Chapter 4 General Grant was talking about the Mexican War.
Except in one case, which I quoted in my post 143.
“The history of the defeated rebel will be honorable hereafter, compared with that of the Northern man who aided him by conspiring against his government while protected by it.”
This is a reference to the Union war on the South. And in the context of the full paragraph in which it appears, it is not favorable to northern actions.
It can be debated why in the world Grant would say the quiet part out loud; that he said it is beyond contestation.
No, it is a reference to the Copperheads, Northerners who supported the Confederacy. That was another bee in Grant’s bonnet, and, as people do, he linked the two preoccupations in his mind and writing.
For Grant, both those who provoked the Mexican War and the Copperheads supposed unjust causes, so it’s natural that he would link the two. He did (at the moment of writing at least) find outright rebels preferable to those groups. Was anything more than that involved, consciously or unconsciously? You’d have to have more evidence to make that conclusion.