I think it makes sense to have both.
RadioButtonGroup is useful when you want a straightforward list of mutually exclusive choices. It handles the layout and selection for you, so I’d keep it for those cases.
For layouts like the one in your screenshot, I agree that individual RadioButton controls would be more flexible. My thinking is to give them a group name so they remain mutually exclusive, while letting you position each button independently and put other controls between them.
That would let you place the three indented checkboxes beneath the first option, with the remaining radio buttons further down. You could then enable or disable the checkboxes when the selected option changes.
Would that cover what you need? I’d like to make sure the proposed grouping behaviour solves your problem before I log the feature request.