It's easier to see commits of a branch grouped together in most history viewers. Even though sorting commits topologically can help, most history viewers don't support that option.

When there is an undesired behavior that is hard to reason about, git-bisect can be used to determine the commit that first introduced it. With a normal merge, it will point to the merge commit, because it was the first time the 2 branches interacted. With a rebase, git bisect will point to one of the rebased commits, each of which already interacted with the branch coming before.

Resolving conflicts in a big merge commit vs in small rebased commits is like resolving conflicts in a distributed system by comparing only the final states, vs inspecting at the actual sequences of changes.