Making a commit with two parents is shooting yourself in the foot, because every other kind of commit can be summarized as a single diff, which means you can definitely do bisect without misery.
What is the simple diff content of a merge commit which solves a conflict between two parents? There isn't one, change my mind.
We both agree that software should discourage shooting yourself in the foot. We disagree about which one of us is using the feature that encapsulates the moment where shooting ourself in the foot happens. It's not nonsense history if it reflects the order that branches were actually merged, which is far more interesting than the order in which commits were written concurrently across disparate branches IMHO.
If you are working with other people that can't read your thoughts, especially those who are too distant to reach you to return the favor when you have inflicted pain on them, they will appreciate it if you rebase your feature branch before submitting your PR and don't send forward an unmerged conflict unless we actually need to talk it over for some reason.
On the other hand I don't know anyone who will be mad that you did this. The rebase feature exists for a reason, and so does amend, reset, squash, etc. How many of these features do you think I shouldn't use? I am only discouraging the use of one feature, the automatic octopus merge that happens when you thoughtlessly run "git pull".
Why do thoughtless things? Don't you want to review the code you've pulled?
Rebasing also guarantees that the commit your CI has tested is identical to the commit that becomes head after the branches merge. How do you guarantee that your branches still function properly after merges? Carefully running the tests by hand between merge and push? My test suite is too large, and we are too busy for that, friend.