Although the Hebrew Exodus story always said that they were there originally and just left. Given that, they were the original owners taking back their land. Its easier to justify taking something that's actually yours. The Aeneas story says that Romans weren't originally from the Italian peninsula and that they took land as outsiders (although, I should point out that they joined up with the Latins so I suppose they were outsiders mixed with natives). Granted, both stories have God or gods telling them to do it and giving them permission, but it seems like deliberately undermining their claim rather than strengthening it.
That being said, as far as I'm aware, none of Rome's conquests were justified as a sort of divine right to the land. They were usually justified as coming to the aid of an ally or as necessary to protect someone from attack. They used (unequal) alliances to incorporate territory into their system rather than simply subjugating and imposing a governor on them. This changed when they left Italy proper and went to Sicily, but any origin myth was irrelevant for Sicily.