They are two separate things, so don't count them consecutively.
She needs to spend 3 out of 4 years in Canada before she can apply for citizenship, not 5. So in that sense, yes, they "overlap"
Let's say she spends 2 years abroad with you. She's fine for her PR obligations, because that's 2 out of 5 with her Canadian spouse. However she does not meet the citizenship requirements, as she was not physically in Canada.
One year can count for both citizenship and PR.