I'v never worn padded shorts, or rather I did once try but prefer not to.
In colder weather I wear ankle length woolly undies with flat seams.
Otherwise I have one pair cycling shorts with the ads unpicked and sticky-up seams, OK for 100km and never tried for longer. Otherwise it's running shorts with flat seams, I've carefully inspected to see where the seams go. Actually, being female and having a dip in the middle of the saddle, the annoying seams are the ones either side that end up under the back of the thigh. The ones that cross in the middle don't bother me so much.