I have an R27 Classic which should be similar in this area to the C28. I have found a bit of water in the two pockets you describe and while I do not know for sure where it comes in I do have a few comments regarding this.
My first thought is that the water comes in from the compartment below the bench seat above. On the R27 Classic there is a storage tray below the bench seat. This compartment has a drain in the bottom with a short hose to the space you describe. I store cleaning supplies in that compartment which often are wet when put in. I have always assumed the water below is from these items. It is also possible some spray could be getting into and around that compartment. Perhaps the C28 has a similar compartment with drain.
Second, and more concerning, is that the stern thruster motor is heavy and unsupported. I found that on our boat there was a bit of movement of the motor relative to the transom. The thruster bolts were tight but I could still get a bit of movement. No leaks but enough movement to concern me. I have since added support for the thruster motor housing. While I have had not leaks from this mount I suggest you check to make sure as it could result in a very bad day.
Third, if you have a stern mounted anode on the starboard side I would check for leaks around the thru-hull bolts.
Finally, there are weep holes from these areas forward to the engine room. Make sure they are not clogged. Unfortunately, even if they are clear not all the water will drain out as the holes are not fully flush with the lowest part of these areas. I regularly wipe up any water down there with a rag or a fuel absorbent pad. I have heard of others having thruster motor failures because water filled all the way to the motor housing.
Hope the helps,
Curt