When I talk about clean headroom and overdrive in the difference between 50 watts and 100, I'm referring to power amp distortion. If you are only going to be using the amp on one (mostly at home), you?re not going to even really hear the power amp distortion that comes from really turning your amp up. Also, most (or pretty much ALL) of your overdrive is going to be coming from the modules. If I were you, I wouldn't really worry about it.
Personally I prefer a separate head and cab just because it's always easier to move. Also, if you are going w/ the single 1x12 the cabinet is a one piece back so it will sound a little tighter. The combo will have a little more low end just because the physical space is larger.