Yes, for me soft saddles and too much padding in my shorts hurts. For me it was a combination of hardening my bottom up, finding shorts with the right amount of padding (not much), and the right saddle (Terry Damselfly). My bottom right at my seat bones still gets a bit sore after about 35 miles, but every ride is a bit better. Good luck! And try to have fun with dialing in. Every bottom is different!
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Embrace diversity: hug a conservative.