The few times I have needed to access the rear hatch cover has not been too much of a problem. I have to go under the well at an angel, but there is enough room for this big guy to deal with access. If I need to remove the switches, they are bolted to the well's/cockpit forward lip and can easily removed with the service loop provided. Note that I have 3 batteries for the twin configuration.
The first page of my pixs shows the cockpit soul. There are 3 access doors to below deck. The starboard acces is where I store an extra anchor and 300' of anchor line, tow bridle, extra fenders and manual bilge pump, plus extra dock/spring lines. The port side is empty because of the plumbing and valves to the pumpout. The 3rd hatch is above the fuel tank and main electric bilge pump. I am not famialiar with the '03 cockpit layout of the CD25. I assume it is abt the same as my '05.
The cable run length as you describe it from the aft helm should not be a problem except as to the volume the cable will take up running aft.
If you go below deck, you have to then bring them up to the batteries, if you have them in same location as I do. This below deck approach means weakening the water integrity of the aft deck with "feed-throughs" for these cables. Would the cost and weight of the extra cable and supports be a factor?
The use of the switches are something you will need to address. Normally they are only used twice on a trip; once at its start and once at shutdown/end. Whereas the helm space may require an immediate access to a resource, such as a backup signaling device, spotlight, etc. This aft helm space could probably be put to better use for these items. These switches will takeup a bit of room, as will the associated cable layout.
If you desire to have some battery control at the helm, you may want to add a single security battery switch inside the console to isolate the main buss in the cabin from the cockpit. I have seen this done as a "poor man's security device". This would also minimize the cales going to and from the the aft helm station. I would suggest the main DC buss be located in the cabin, out of the elements, behind the helm.
Boy, did I get windy on this.

Hope this gave you some food for thought. I just got my camera back from the factory. If you need any better pixs to show you my setup, I should be able to get them within 2 weeks. I have my Saturdays to do this.