Well thought out! I like that! IMHO, there's nothing wrong with a 'wing type' (as you call it) swim step/platform on one side. I'd go with a thru-hull transponder or put your transom type under the swim platform side ... kicker on the other. As far as weight and balance go, keeping in mind that 2/3rds of a planing hull is forward of the CG, you should take into careful consideration all that goes f'w'd. If you are going to highly-outfit the boat for almost live-aboard accommodations, then it may mean a disproportionate amount of weight ending up f'w'd of the CG as mentioned. Using those 'wing type' swim platforms and the main on a bracket to move it aft, then that's an opportunity to help move the CG aft if your accommodations are moving it f'w'd. This is true more so for the Kodiak, which was designed for 'commercial or serious recreational fishing" ... in other words, more stern weight capacity.
A good way to estimate your CG location is to look at the 000x series of drawings that come in the plans and study the construction details very carefully ... if you build the boat exactly as shown in those drawings, it will trim 2-1/2" up at the bow. Whenever you add something heavy f'w'd of the CG that is in excess of what you see in the 000x drawings, then figure out a way to counteract it with weight of some sort behind the CG ... compare moment-arms. Here's an example:
Consider a boat that's exactly like the one in the 000x drawings and add a 70# anchor winch and 50# bow-thruster to the bow (about 19' forward of the CG more or less). The newly-added forward moment-arm of those items is 19' times 120#, about 2280 ft-lbs. To counteract that, move the 100# of batteries that are right behind the aft house bulkhead aft to the transom and put the main motor on an 8" bracket (0.66 feet). Assume the bracket weighs 40# and the motor weighs 500#. Complex, but here goes. Removing the batteries from the house bulkhead reduces the forward moment-arm by approximately 3 feet (they were ahead of the CG by 3 feet) times 100#, about 300 ft-lbs. This reduces the bow-down moment of the battery's original location by 300 ft-lbs. Adding the batteries to the transom (inside the transom about 8' behind the CG) creates an additional bow-up moment-arm of 800 ft-lbs. The net result of the battery move is an 1100 ft-lb bow-up moment change. Now for motor and bracket. Bracket is about 9' behind the CG and weighs 40#, a 360 ft-lb bow-up moment. The motor's original moment-arm is 9' times 500#, or about a 4500# bow-up moment-arm. Moving it to 9.66 feet further aft gives it a 4830 ft-lb moment for a net increase in a bow-up moment of 330 ft-lb. The net trim change in bow-up moment is:
-2280 (anchor winch and bow-thruster) + 1100 (battery move) + 360 (added motor bracket) + 330 (motor move), or about a net -490 ft-lb bow-down trim. Considering the boat likely weighs 5000+ lbs on the water, this likely won't cause a large bow-down trim. Perhaps the original 2-1/2" bow-up trim becomes a 1" or 1-1/2" bow-up trim? That would be fine. But NOTE that if you used a 100# bow-thruster and a 150# big commercial anchor winch, their bow-down trim would become 4750 ft-lbs ... an increase in bow-down trim of 2470 ft-lbs ... a ton and a half! THIS is why you really want to pay attention to WHERE extra weight is added and how well you've balanced it out. Seemingly small decisions can make big differences. This is because the GA is light for it's size ... making the boat half as expensive to build compared to one that weighs as much as a commercially-manufactured vessel, and giving you double the gas mileage so your boat can have an extended range and reduced cost of operation. It's a fair trade. A commercial 10k lb boat would not notice changes in the locations of items that a 5k lb GA would.
I retire as of March 1 ... high on my list is the creation of models and spreadsheets that will allow me to help builders dial-in their boat's layout in a most optimal way. Also on the list is a fine tuning of the Standard and Kodiak GA's, now that they've been on the water for a long time and we can see what the typical usage is, designs around a slightly different weight arrangement. NOTE that this will be a MINOR improvement in the designs ... the main issue in terms of trim is the boat's light weight combined with the fact that planing hulls have 2/3rds of their weight forward of the required CG envelope. This is why live-aboard boats are DISPLACEMENT hulls rather than PLANING hulls ... a boat that's required to plane requires careful considerations and is by default more sensitive to things like weight distribution. There are some beautiful live-aboard type accommodations in several GA's out there that demonstrate that it's possible. You just have to pay attention and tune as you go. Note that the Kodiak addendum document lists several ways to move the CG around should you need to.