Another consideration in favor of Apt 1 is Harry possibly taking more of a leadership role in the Commonwealth. If so, is it possible that Harry and Meghan may need more formal entertaining space for visiting dignitaries?
Harry could and would continue to host events where he does now. The apartments that belonged to Diana were converted to work space for their foundation. There are 2 large reception rooms for use of hosting for the foundation. There are also the state rooms of the palace available for such.
The palace has a high level of security. Privacy and security for the kids in any part of the palace would not be a concern.
There is also the much higher expense of renovating two different apartments. Harry and Meghan are not going to just move into the Gloucester apartments the way they are. There would need to be re-worked. And then accommodation would need to be prepared for the Duke and Duchess. The queen isn't about to dump her cousins on the street for Harry.
I notice Princess Michael is quick to suggest the Gloucesters move. I don't see her offering her own apartments up to anyone.
I do think we will see London being Harry's home base, and 4b (possibly combined with the apartment next to it) is the most likely. And a second home on one of the royal estates.
I still find it unlikely we will see a new country home purchased for them by Charles or the queen which would have to happen for the Cotswalds or such. Harry isn't about to spend his trust on a house, as that is the money he lives off of (interest from trusts/investments). If they choose to have a primary home in the country, and a small apartment in London (like Edward, Andrew and Anne) then I see them possibly leasing from the crown, in Windsor. Or if Charles does buy them a home, it would be as this, their primary home. If they choose this option, there is no need for the money and time to go into a larger KP residence.