I agree that would be too low to cut it for me. You top it where you want the first side branches to start. However, it should still grow fine and since it's a seedling you don't have a graft to worry about. The lower branches will drag on the ground, but maybe there is a way to prune to correct that later. I don't know.

Put it in the sun. It needs lots of it.

If you keep it in a large pot, then it works out well; the branches will be low to the ground. Otherwise, you'll just have a tree with a very short trunk in the ground. It'll be fine.

Can anyone help me with advice on how I should prune this pickering mango?

Looks fine. If you changed your mind...just pinch off all but one new shoot. Stake that one shoot and you have a new leader. You will never see a difference in a few years or less.