There has actually been extensive discussion by both the crew and forum members on the feature of the Synapse to which you are referring (moriond help with references!). The long and the short of it is that it is NOT a design flaw of any sort that would need to be mitigated. Rather, it is a morphological consequence of the complex design of the Synapse pockets. Because the pockets are so difficult to construct, they must be done in several pieces, the shapes of which leave two spaces at the corners of the side pockets.
Any water problems can be head off by:
1.) Getting an insulated bottle such as a Kleen Kanteen or Hydroflask
2.) Using a stuff sack or other bag as a liner in the water bottle pocket to catch condensation
3.) Putting the water bottle in the bag when it is already at room temperature (any bottle that is condensing in your bag is already getting to a state of lukewarm before you drink it anyway. If you were able to drink the water cold, there would be nothing left to condensate).