I think the difference is that, as you say, Märtha Louise chose to become a private business person as opposed to a working member of the royal family. I think that precisely because of the small size of the Norwegian Royal Family, she would have been very welcome to had she wanted.
When she made that decision, she left the Royal House and gave up her HRH. I suppose it was decided, that for the next generation it would be easier for Sverre Magnus not to be a member of the Royal House or have an HRH title from the beginning. It makes things a bit clearer. I think they've made it rather obvious that he is not expected to take up royal duties as an adult but will rather choose and make his own career.
The question of spares is a difficult one for all of royal Europe. I think it is nice for Magnus to know that he can choose his own path in life and not be a spare until he's basically "no longer needed".
On the other hand, even for a country with a relatively small population, I think the Norwegian Royal family have gotten themselves into a spot where the whole workload rests on the shoulders of 2 octogenarians and one other person = Haakon, with Mette-Marit being ill and unable to conduct too many duties. It will probably mean that Ingrid will have to step up young but there might also be a point at which Haakon will have to almost everything by himself. So there is also that.
By the way, I don't think it's that Märtha Louise would be incapable of conducting royal duties. I have watched her, she was raised a Princess and it shows. She knows quite well how to conduct herself on engagements and what to answer in interviews - if she wishes
. It's that sometimes she does not wish to conduct herself in that way
But even if she wanted to, which I don't think she does, as long as the shaman is her partner, I don't think she would be acceptable to the Norwegian public as a working royal.
Notably, I believe she hasn't done any public engagements since the shaman scandal erupted last May, before that she always did some in addition to her private career.