Although there is some overlapping of the individual octagons in a strip of octagons, it is still not severe, and is outweighed by the versatility of thye resulting octagonal flexagon. In any event, it is the relationship between successive hinges which matters in a flexagon, so the remainder of the polygon can be rearranged to suit convenience or aesthetics.
If it is considered important to preserve the full symmetrical polygons, they can be cut out individually and pasted toggether. Once the strip is folded, overlapping will no longer be a problem. If rapidity and efficiency of assembly is preferrd, corners can be cut but the flexagon will still work.