i had a very similar dilemma on a significantly smaller scale. i have a 6 mile one-way commute on days when i'd need a laptop.

in any case i went with whatever i had read would get me through most any condition i would face while commuting but not touring. i went with ortlieb sport packer plus as a pannier but i also picked up an Ortlieb office bag.

i always have one pannier on my bike on the left side at all times. it contains my rain gear, sweater, u lock and a beanie. i throw my lunch it on top of all of those things.

i only need my laptop one day a week so its not a big deal to bring it. it usually holds my laptop and school supplies plus clothes. i put this one on my right hand side. the ortlieb office bag has a roll top and is completely waterproof.

on other days, when i'm not commuting to school, i use both of teh sport packer pluses and carry my clothes and dress shoes on my right hand side. the sport packer plus doesn't have a roll top but is still waterproof however, its not as waterproof as a rolltop in the sense that you can't dunk it in water and it will float like the roll tops do. so i guess if you went with panniers, the roll tops are waterproof but for commuting - overkill.

i also think that your idea to get a grocer pannier and throw a backpack in it, is a good one but putting your bag in a dry bag in a pannier seems redundant when you can just get a shoulder strap for a pannier and carry your stuff that way.

i hope that helps.