A good commit means a good version. That's what we're doing after all: version control. Every commit you produce should be a valid standalone version of the software. Commits can build on each other, e.g. you can add feature a then subsequently add feature b that depends on feature a, but a maintainer should always be able to only take feature a, there shouldn't be bits of feature b in there, and there shouldn't be fixes for feature a in feature b's commit.
With practice you can learn to make rough commits first then clean them up into proper commits later. For example, there are "end of day" commits and there are fixup commits. Those are both valid uses of git, but you shouldn't be exposing those to your team. You need to rebase them before sending them. A good git user will sow the seeds for a smooth rebase early.
git add --patchI don't need line-by-line usually (but it can technically do it if needed), but undoing accidental adds is indeed a bit of a pain.
Ultimately, I don't care what tools people use if they produce quality work and can integrate with the team without creating additional friction. There's nothing that says that a good GUI can't exist, or even be more productive than the CLI in some cases. I have had enough experience of GUIs causing problems, however, to make me nervous when I hear one is being used by a team member. It's often followed by something like: "I ran into a problem with Git, so I just deleted the repository and cloned it again."
Perhaps it's time for me to start looking at the available GUIs again, so that I can make a recommendation for a solid one when someone doesn't want to use the command line. In the end, though, one still needs to understand Git's behavior, to some degree, to be productive and avoid creating situations which take the team's focus away from our goals. I don't know that any GUI is going to help junior developers with that.