I remember reading somewhere that using a slightly incline, even just 1%, more closely mimics an outdoor walk or run. Even here in AZ where it's quite flat, you do encounter the tiniest ups and downs. So yes, I do always use the incline. But unless I have it set pretty high, I don't feel like it's truly a lower body workout any more than a regular run or hike would be.
In answer to your specific question, I would personally probably do the incline walk or run AND lower body, and then only upper the next day, giving my lower body a rest.
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