Can you eat apples with spots or scab? Look beneath the skin
The photograph shows dark marks that could resemble scab, but you also describe brown, soft, mouldy flesh beneath them. That is the difference between blemished skin and an apple that should not be eaten.
Dark, scabby marks on the skin can sometimes be only superficial scab, in which case the blemished part can often be cut away. But you describe the flesh beneath these marks as brown, soft and mouldy. This is no longer just about the skin; the fruit is rotting. As you want to eat the whole apple with its skin, the advice is not to eat this one at all.
The photograph shows several dark, sunken patches. Together with your description, that fits an apple to discard rather than one with purely cosmetic marks. Throw this apple away and check the rest of the crop individually: firm apples with only surface blemishes can be used straight away, but discard anything soft, oddly smelling or brown inside.
In September, it is also worth removing affected apples from the tree and ground so that they do not remain as a source of infection or attract further problems during the rest of the season. Use the healthy apples first and store only those that are intact and firm.
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