You've pretty much hit the nail on the head and now understand why the autopilot was created. In life, you can pretty much make anything work. People started with basic paddle kayaks, then pedals came out. Then people realized you could add motors. Handy people mocked things up with what they had. And then, an industry was born. All of the options you talk about can be done and every one has a drawback. Like you said, by the time you add it up, you might as well go whole hog. You either stick with a good PDL or you go whole hog and do a full trolling motor based boat.
Couple things to help you down the path. Once you're on the water, having an autopilot is awesome. It is a fishing machine. If you fish offshore, then spotlock is great. If you beat the bank then cruise control and navigation is perfect. You know when you hook a fish in your boat and he pulls you just as much as you pull him and you end up in the cover you're fishing? A quick spotlock fixes that (I know you can pedal backwards too).
Speed is not the bag of a kayak. If speed is your priority, then you need to get a bigwater PDL or similar water cutting kayak and not a barge like the autopilot. The bigwater with pedals will do 5.5-6 mph. The autopilot tops out at 4. That's all due to hull design.
You're pretty close on your amperage calculations. On full speed the autopilot (45 lb thrust) draws 45 amps I think and does 4 mph. For the 2 miles you want to go, that's a 30 minute run and you're going to burn 25 amp-hours. On a 100 ah lithium that's roughly a quarter charge (you have 90% of the stated capacity nominally). And you'll have that getting back, so you've burned 55-60% of your battery in motoring. The remaining 25-30% of usable charge is plenty to fish around and spot lock in place. Spot lock takes nothing unless you're in current. If you were motoring and then using your pedals for fishing then you'd be in the same boat.
If you go with a motor, a 100AH lithium is your starting point. I have an 80 and can get by because I fish a lot of smaller water and I have a battery meter to keep an eye on. I wish I had just gone 100 and I'd never worry.
If you go autopilot, just get the 136. Its 4 lb heavier but you get 12" in front cockpit and 6" in the back well. Its marginally faster by 0.1-0.3 mph from what I hear, but I can't confirm that.
The only functional downside is the size. Its a big boat and a heavy boat. Its closer to a boat than a kayak at times. I can mostly use boat ramps to launch from the bed of the truck, so I only have to lift it in and out semi empty (battery and seat in the boat, motor and gear already removed and in the truck). Even still, its 150 lb that I'm moving If you're loading it with the motor and your fishing gear, it's a 200 lb boat to move on a kayak cart. That's a lot.