It's been said repeatedly that the two lines will operate independently from each other because MSC wants Explora to consistently deliver better service, and I think that makes sense. But from a corporate strategy perspective, I assume a big reason for operating as two companies is that it makes an eventual sale (full or partial) of Explora or MSC easier.
MSC is doing a ton of the heavy lifting to get Explora off the ground, and they probably want to eventually see the benefit of that work. As an example, they may be able to later sell something like 10-20% of the business, then take those proceeds to fund the next round of ship expansion under the MSC label.
Of course, they may not ever do that, but typically from a strategy perspective, you'd want to leave as many of those types of options open.