I fail to see what is user friendly about Monticello , I find its GUI and the total workflow really bad, certainly the worst VCS GUI I have ever used. But I will admit this is my personal taste and my opinion that can be safely ignore.
StHub on the other hand is whole different situation.
My criticism about StHub unlike Monticello are not opinion based, they are fact based, StHub is unmaintaned , with the usual failures prompting Esteban to reset the whole thing and lacking the most fundamental features like a sophisticated search facility and any form of browsing. I could go on, but I think the shortcomings are obvious. That's no bashing, its a statement of facts.
On the subject of file based code, I wonder what you use for Pharo VCS because the default Pharo VCS is basically zip (mcz extension) files containing source code files , the usual text files with the "st" extension. If you mean the fact of actually worrying about the files themselves, the only worrying you do with Git is for the gitignore file (if you actually use one) that basically there can be listed what files or directories should be ignored by Git. The rest are done automagically by Filetree, GitFileTree or in my case my Git GUI client.��