Hydration port on a pack bag vs. running hose out the side of a roll top closure?

You might be over thinking it just a teeny, tiny bit. I would personally go for the port because its more convenient. I don't think that a port will significant compromise your waterproofness unless you want a bag you are going to submerge.

If you plan to use a hydration system, than have the port done. If done right, it won't leak.

Trying to roll the top up with the tube sticking out of it would likely affect the top's ability to keep water out of your bag, and make for an unpleasant drinking experience at the same time.

Remember, rain water that hits your bag top and drinking tube could potentially follow the tube down right into the bag, no matter how rolled up it is.

Gravity does not always offer the the path of least resistance for water.

I'd just go with the ports if you feel like there's a potential of using a hydration bladder.

Michael, in your place I'd ask Seek Outside to put in the hydro port. I've run the hose through a rolltop on different packs, and I find it a nuisance.

I know Kevin Timm prefers to put a hydro bag outside the main bag in case it leaks. He does have a point; with Xpac if you do have a leak you won't know about until there's a big lake in the bottom of the bag and it starts leaking (very slowly) out the bottom seam (been there..). Personally, having water weight anywhere other than next to my back is intolerable, and I'm willing to take the risk. Use a good bladder and be careful to screw the hose on tight. I use heat shrink to secure the hose to the bag, just in case.