Both kayaks are great choices. You will not have issues with the stability of either kayak, in some ways the Autopilot 120 might be even better. I'll explain.
I used the SS127 for the past few years and it was a very well thought out kayak. It also has secondary stability that matches or tops anything on the market and one of the better seats. I could step on the side and I might fall in the water and push the kayak away from me, but it won't flip. The PWR 129 seems to take the best of the SS127 and make further upgrades and improvements in terms of rigability. I don't care for the rudder design much as others have said, I tend to drag my kayak from where I take it off the trailer to the water if I'm on grass or sand and with that design, you'll be dragging it on the rudder and not the drag plates. A cart is a must. I didn't have many issues with anything breaking on mine, but the pads don't hold up well, the one at my left foot tore and the seat pads don't stay glued in place. I've heard from several other owners that theirs blew off on the way to the lake. What I found worked the best was double sized tape - I always kept a roll in my truck and some sandpaper and restuck them every couple of outtings, which was annoying. Also I would have to tighten the handle a couple times a year, because it does come loose.
My kid had the Old Town Topwater 120 for the past few years. The seat on that was rather lacking (it's better on the Sportsman line but not as good as the Bonafide). It didn't allow for the nice little things like the ability to mount the fish finder on the dry pod and have a center mounted fish finder and not as many places to set a rod down in front, although the rod holders on the front sides do work and are also great for rigging on the water. One thing I did like a lot better about my kid's Topwater 120 which should be the same hull as the Autopilot 120 is the performance. I could paddle it about 1mph faster than my SS127, it was almost as hard to flip but it was much less rickety on choppy water, which was great for me since I have terrible balance. There also a ton of storage space in the back, you can fit a 16x16 blackpak pro and a small ice chest and they're accessible - due to where the bungees on the SS127 were, if I put a cooler back there it was behind the Blackpak and I couldn't reach it.
We both now use Old Town Bigwater 132 PDLs. The Bigwater is designed for speed, probably the fastest pedal fishing kayak on the market now (some say the Salty is faster). Navarre Kayak Fishing sells a lot of great upgrades, including a "dashboard" which you could probably mount your fish finder on. The scupper transducer mount is great and keeps my transducer protected from anything it might hit and side view still works as far as there's any light.
My kid did flip his kayak once, intentionally. We went out on the St Lawrence with no gear just to scout it out and see what to expect and we were in a shallow and still cove so he decided to flip it since he had nothing to lose. My other kid took this video right as he went over, but he probably had it rocking for a good couple minutes before this, it took a lot of work!
Ethan Flipping his Kayak.mp4