Flats vs Clip less for long distance.

I've been riding clip less all last season and until last week I decided to switch to flats. Last week I decided to switch to flats to see if I can improve ride comfort. I was surprised during my first ride. It felt weird and I maintain the same technique as if I was in clip less minus the pulling up the pedal. I noticed that first couple of rides I was struggling to place my feet, trying to find the "perfect spot" but then I forgot all about it and it became second nature. I didn't do long ride in flats yet but I rode bunch of smaller efforts during the week to combined 378km. I feel like my feet are changing positions during the ride depending on terrain and my saddle position (going up, down or during standing). I believe this change of position allows better comfort. Does anyone have similar experience or its just my bias or poor bike fit?