Hello Donny,
Ah, Bonsai - That had some good features, for its time. The feature I miss most is the ability to control the default values of parameters for new items, including choosing whether to inherit start or due dates and contexts from a parent or sibling item. Over to your questions, though:
MLO effectively does have the note feature, but it's probably confusing you by calling it a "folder". Folders can store your notes (and that's something I use them for) but they are not tasks, so they can't be checked off of have a % progress value. If you find the folder icon confusing, you can even go into Tools - Options - Automatic Formatting, then change the "folder" rule to show a note icon or something else.
MLO has a progress bar for projects, which you can switch on and off under Tools-Options-Themes & Formatting, then selecting "Tree format" tab in the pop-up window. It doesn't look like the Bonsai one, though.
I hope that helps,
Stéph