For long-lived feature branches that are the target of multiple smaller PRs, history should never be rewritten. I call these branches integration branches. I agree with you wholeheartedly that master should be merged into the branch. It's also so much easier to resolve merge conflicts all at once in the merge commit rather than iteratively for each commit. Also, the information on how merge conflicts are resolved is then preserved in the merge commit. It's critical however that when you merge the branch back into master, you use --no-ff. It gets really confusing when you fast forward master to the feature branch.
The solution for it being ugly is to look at main/master's history with the --first-parent option. This lets you cut through the noise and just see the true history of the main branch. Without --first-parent, you see a bunch of commits in the log that master was never actually pointing at. This is why it's critical that you use --no-ff when merging these 'integration' branches as I call them. It's important that the integration branch is the second parent of master.
But what you are describing still isn't good enough for a lot of people, because even though `--first-parent` hides the noise it's still there and just knowing there's a mess under the rug is enough to be problematic.
I don't think it's really the fault of the tooling, moreso with what is a common interpretation of what is a mess and what isn't. If the github commit history allowed you to show `--first-parent` maybe it would be less of a problem.
Yes but if it's a shared branch then you may have problems with this.
The safer way is to merge from master into the branch but nobody wants to do that because it's ugly.