Despite appearances, "it is the chances" is not a phrase. "what with space being the mind boggling size (that) it is" is a parethentical phrase pointing out that space is mind-bogglingly big, which explains the very small chance of being picked up. "what with" is an idiomatic expression used to introduce an ancillary or explanatory fact.
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silak12I guess apart from your definition of "what with" the following definition might be applicable here as well.What with = Taking into consideration, because of, as in What with all you have to carry, we should take a taxi.Yes, this is the same meaning.