Mara Serena is a nice lodge, good choice!
It is not a must to book a package through a third path, there is no such rule. All depends on individual people and complexity of your trip. Yours sounds very straightforward: Nairobi - Mara - Nairobi, nothing complicated.
Usually people involve a third party for a) price, b) transfers between lodges/camps, c) suggestions of itinerary. If price is to your satisfaction (direct price may or may not be higher or lower than a third party) and transfers are taken care of by Serena (eg road transfer from Nairobi to Mara and back) or you took a flying package or booked flights directly with Air Kenya or Safarilink with Serena picking you up at the airstrip, you have nothing to worry about as your itinerary is simple. People put together much more complicated ones themselves too!
By the way, Serena Nairobi is a nice hotel centrally cituated in town, check with them if they give you a good deal if you are staying in their Mara property - worth a try anyway!
So, three reasons: 1. Price, 2. Transfers, 3. Itinerary - if all is to your satisfaction, book and enjoy your trip to our wonderful country!
I am sure the will be a lot of diffent opinions and advice - people here are very helpful, but the choice is yours!