Adjusting the stock suspension does not change the seat height at rest. It will play with the sag. If you swap springs but maintain the stock uncompressed spring length, the seat height will be the same. If you replace the stock shock with another shock of unequal eye to eye length, you will change the seat height.
EDIT: One thing to keep the butt nice and comfy on long rides are biking shorts. I discovered that using my racing bibs not only makes it 10x easier to get in and out of sweaty leathers, but makes my butt hurt a lot less! I never realized how much they helped until I rode without them for more than 2 hours.
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