The difference rides on the distinction between whether the term in question is a proper noun or a common noun.
Because "the Universe" is deemed to be a singular, unique entity, and because "the Universe" is the name of this "unique celestial object" (phrase from Chicago 14th ed.), it is usually capitalized.
There is some fuzziness here in the same way that there is fuzziness with earth/Earth, as in:
As we orbited, Earth shown brightly below.
He picked up a clump of earth and threw it at me like a baseball.
So, when talking about the [one and only] Universe, it gets capitalized.
The "observable universe," however, is easily shown to be a common noun by simply brining attention to the fact that there are as many observable universes as there are observers.
In fact, the very point of calling it the "observable universe" is to highlight it's incompleteness as a concept and its commonality in terms of how the concept is asserted. Conversely, the purpose of referencing "the Universe" as "the Universe" is precisely to assert it as an existential reality that is immutable relative to perception (whether commonly shared or not).
Referencing "the observable universe" is something quite different from saying something like: "Welcome, to the Moon! Behold, ye, our beloved and now observable Earth!"