List under construction ....
Does the Synapse 19 still have this issue (that if the water bottle spills, it will reach the side pockets)?
I don't know if the 19 is the same as the 25, but in my Synapse 25, the fabric that divides the center pocket from the side pockets is elastic mesh, so water or moisture can be expected to go right through it, holes or not.
My drink of choice is tea so I use a Zojirushi insulated tumbler (aka Thermos) with a locking top similar to this one which fits into the Synapse 19 quite nicely.
Amazon.com: Zojirushi SM-KHE36AG Stainless Steel Mug, 12-Ounce, Smoky Blue: Kitchen & Dining
There are travel mugs/water bottles which are lighter but I find the leak resistance and excellent thermal insulation to be worth the extra weight. It has a smaller mouth size compared to an insulated Kleen Kanteen so I wouldn't use it for soup like Tynan uses his Kleen Kanteen.
I use something very similar, but it's 24 oz so I can carry more coffee with me. :) It fits perfectly in the water bottle pocket of my Synapse 25.
Thermos Stainless King 24-Ounce Leak Proof Drink Bottle
I use insulated mugs and water bottles from Contigo. They have an "autoseal" feature that keeps the liquids inside from accidentally spilling out. They even have a locking version if you are really paranoid (which I am :)).
I ended up buying a small backpack from a totally different maker due to this thread. That bag has the hydration pocket segregated from the other parts of the pack and drains straight out the bottom. Thank you to the OP for the heads-up!