"Tell me you don't have to debug foreign codebases often without telling me" ;)
The primary value of commit history comes from blame, bisect and corresponding commit messages. There's no reason to "treat PRs as atomic changes to the code base", commits are already supposed to be that and PRs are groups of commits (sometimes groups of size 1, but often not).
> When I mean "squash on merge", I mean the commit history is fully present in the PR for full scrutiny.
And when you merge the set of commits prepared by the author for review in, you get both "summations" and individual commits stored in the commit graph (where their place is) and you get to choose which way you want to view them at retrieval time without having to dig up things outside of the repository. Sometimes it's useful to see the summations only ("--first-parent"), sometimes you only want the individual atomic changes ("--no-merges"), sometimes you want to see them all but visually grouped together for clarity ("--graph"). When you squash on merge, you just give all that flexibility away for no good reason.
It's a commit graph, not a commit linked list, so treat is as such.