だ and である are really two forms of the same verb, which is a very odd and irregular verb. There's not really a benefit to thinking of them as separate, as every other form besides です～であります is shared between the two. Having two options for the shuushikei is only one way this verb is unusual.
In terms of the mizenkei, I'm not sure it even has one. で is the ren'youkei, but ではない as a unit (sometimes without the は as でない) is the negative form, which isn't formed off of any mizenkei, it simply is on its own the negative form. Etymologically, it is from the ren'youkei + は + ない, much the same way as adjectives are topicalised and negated - c.f. 早くはない. (でない, without the topic marker, is formed in exactly the same way as adjective negatives are.) At this point, though, it's basically a unit, and there's no sense in arguing that it's still used as a multi-part construction.
To answer your questions directly:
- Yes, technically, putting で in bold there is demonstrating its use as a ren'youkei, but that's not really a helpful way of thinking about ではない anymore. It probably would have been better to put the whole word ではない in bold.
- There are not two ではないs, because だ and である are the same verb. ではない is an irregular negative form that's built off a ren'youkei + topicaliser combination, rather than a mizenkei (or an adjective-like plain ren'youkei).