Agreed on sooty blotch, the dark sunken spot with the black center doesn't look like scab to me (at least not the way I normally see it present) It does look just like a type of rot we often get on our honeycrisps during wet years; but that normally shows up much later in the season....close to harvest. I don't know the name for it, but generally the apples are still harvestable and we just cut out that section. It usually has well defined edges and a narrowing cone of mushy rotten apple extending down from the surface. My experience with bitter pit is a tan "corky" area under the dimple in the skin, and a Spartan says it gets worse during storage.

I agree with Keriann. Yes, you should really let them dry out. Matter of fact, once my seedlings are as big as yours, I let them dry out pretty much all the way before I water again. You can tell they need watered when you pick up the flat and it feels light as a feather. Then after you water, it's much heavier. Your method of bottom watering is quite unique, I must say. I think that most folks bottom water the way I do, which is to say setting the cells or cups into a tray of water and letting the plant absorb as much as it wants until you see moisture on the surface of the soil (usually takes anywhere from 5-20 min). Now, I can't say for sure what positive or negative effects your method of watering might have, except that it sure sounds like a pain in the hiney to me, and I somehow doubt that the soil is getting properly saturated. You want to simulate mother nature; a soaking rain. Then you want to let the soil dry out. That's how it is in nature. Roots need water yes, because the plant needs water, but then they need to dry out and get oxygen. Damp soil all the time = no oxygen to the roots. Now, I can't say for certain what part of your program is causing your issues, but I would start bottom watering them as described by letting them absorb water sitting in a tray. I think you will find that using this method, you should only have to water every 3-4 days, or less. I would lay off the ferts for a while, and then make sure only to fertilize when the soil is already damp, or you will burn the roots. I just mix the fert with water, then pour into a tray and bottom water as usual. Give this a shot, see if that doesn't help.

Orchid leaf

I'm not finding photos of necrotic blight, but other blights show darker spots with a circular pattern not seen on my leaves. Also my fruit is unaffected. Septoria Leaf Spot sounds and looks similar to what mine have. Either way, the treatment is removal of affected leaves and a copper spray. I will do both as well as a preventative spray on my other tomatoes. Thanks, Omni.