Adjust whatever you need to as you develop the specific muscles you use cycling.
Because your legs aren't used to the load, you are sitting on the saddle more ... and most road bike saddles aren't meant to be seats, more like perches. Also, your lower back and stomach have to do a lot of work which leaves you either leaning on the bars (hurting hands, wrists, elbows) or sitting on the saddle more (which you already fully understand.)
Flat pedals are good for confidence as you get used to riding again. Lowering the seat a little will get you using the portions of your thighs that you normally use .... you will lose a little power but your legs will probably have very little power at more extension anyway, until you ride some more.