I think you very much nailed it.
Plus that Alexandra was still a princess.
The mother of the oldest grandchild at the time.
And still very popular.
It would have been unacceptable at the time not to grant her some kind of income, as she could not hold a "normal" job, being a princess.
The change came when Christian was born and when Alexandra later remarried and lost her princess title.
From then on you can argue that she should not have an apanage.
The amount is all in all still fairly trivial, but she is not seen as working for her money and she's (on paper at least) getting a higher apanage than Mary, who works much more and holds a much higher position.