One of Atlus' demands was that it would be able to keep operating as always, so I'm hoping Sega is only there to sort of back them up. Though with Sega's financial situation I don't get that either. As long as Atlus can keep doing their thing (Persona 5, localizing obscure stuff, etcetera..) I don't care if Sega uses Atlus characters in their Sonic games or whatever.
Also, the interesting thing about these two companies is that Sega is notorious for not localizing their more niche franchises anymore (Shining, Valkyria Chronicles, possibly Yakuza from now on) while Atlus is the exact opposite.
Worst case scenario:
Sega pulls the plug on western releases of Shin Megami Tensei etc.
Best case scenario:
Atlus gets to localize stuff like Yakuza 5, Yakuza Ishin, Valkyria Chronicles 3 (or 4) and so on.