I started with a lake troller mounted on the track of my Old town.  Lot of flexing and bouncing, didn't like.  Now have a uni-troll (probably overkill, but it retrieves fast) on a V-lock mount bolted to the hull.  Much better.

Highly recommend the most solid connection to the hull you can to handle the bouncing weight.  I'm not sure you could do this with a direct mount to the inflatable.  Probably need some kind of mounting platform that gets strapped down.  I know that is not what you want to do.  I fished from an inflatable for a couple years and this is how I had things like my rod holder and transducer mounted.  I would also really evaluate how you're going to travel.  An inflatable fits in a smaller place (somewhat and still not small,  picture a fairly large trunk or suitcase), but a roof rack isn't too intrusive and hard kayaks are way more fishable than inflatables.  (no direct experience with the Hobie pedal ones though)