Because if you are running a campaign with "too many" imperial players, it could make sense to declare some of them as traitors (this is a written suggestion somewhere in the campaign section) - then they are using the imperial ships, but are chaos "fluff wise" - and so you could have ships that follow the imperial fleet lists, but are roling on chaos tables.
And, according to FAQ chaos fleets can include a small number of imperial ships with reduced LD.
But yes, in the most cases this result can't be applied witch mean it has to be re-rolled.
PS: Fluff wise, every faction exept tyranids and necrons could be chaos and use these tables, if your campaign allows stuff like that.
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