I totally agree. I've never understood the push back against clean "railroad tracks" (i.e. rebasing instead of merge commits). It's simple, scales nicely and gives you a lot of options. Once you start allowing merge commits in the tree, things can get messy but with a bit of discipline, it elegantly solves every version control use-case I can think of, or have encountered, including at scale.
If you have a large PR with multiple nontrivial commits I think you should merge it so the intermediate states are the same ones that were originally tested. Otherwise you could break bisects, among other issues.