Stem rot ?

No its normal, it is just the way the stem Looks like if it was underneath soil before. The soil washes down each time you water, espacialy when you got a lot of run off. Just add some soil on top and you wont See this part of the stem, or just let it be. Its nothing to worry about.

maybe stained by fertilizer and erosion exposed it. Or when you irrigate is there a pool of water that high on the stem? same idea. is it slimey? Extra soft/mushy? does it stink? I don't see any fuzz. if not, probably fine. proper watering habits and a well-constituted substrate will avoid nearly all self-inflicted rootzone problems. Allow a proper wet-dry cycle and you'll be fine. Always saturate entire pot, but need to let it dry some minimum amount before repeating. Early on i'd suggest 1" deep. This exaggerated wet-dry cycle will promote more robust roots early on. Can increase frequency slghtly later on, but still want to the top to dry if you want to avoid algea and such growing on top. I wouldn't go less than 1/2 weight loss, but the frequent fertigation setups do 30-33% weight loss between -- this is with well-constituted soilless substrate and a well-sized plant to allow it.. not something you can whimsically do. 50% perlite for anything soil-like as far as water capacity. Coco only need 33% becuase it holds 2/3rds the water per volume. Both mixtures end up with similar gas:water ratio which is the what matters not what solid material you chose to use for the substrate.

That doesn't look.iv only ever seen Pythium,root rot on seedlings,if that's what it is and not for over 10yrs as I use microbes with my seedlings.The good bateria eat the bad. I'm not sure though.Your soil is very wet and needs dry cycles.The top layer "half inch" needs to dry out completely so if you've kept it wet the whole time this will be the causes.The plant looks healthy though.I'd get some microbes/bacteria from the shop if poss if mot out of the garden and brew some compost tea.Ecothrive do instant tea called Biosys that doesn't have to be brewed if you haven't got an air pump.