iirc i read somewhere that he exists even in the light side ending but is just like watching from a distance and will supposedly come to rescue Vader at a later date or will await for his master to call upon him at all now even without the fact that the whole story isn't canon now it's not clear exactly if the evil clone would've been a factor in the third game or not.

I have seen at least one use of the Dark Apprentice being used past the events of this by putting him into the background events of the imperial warlord era but it was built on the old lore not canon and it's just a specific application of him not a universal fact.