With the polyembryonic mango seed, if the patent applied to a mango variety with the characteristics ABCD, the clonal seedling would also have the characteristics ABCD and would be indistinguishable for patent purposes. A zygotic might be ABCd if you are lucky, who knows if that would infringe the patent. I guess it becomes ABCD$$$$$ vs ABCd$$ ??
While a patent does describe certain plant characteristics, it does not prohibit you from growing a plant with even identical characteristics, as long as you didn't produce it via asexual vegetative reproduction from the patented variety.
Growing a zygotic seedling of a patented plant is pretty clearly never patent infringement (other than GMO gene patents, a different issue). This is true even if the seedling and its fruit are indistinguishable from the patented variety.
On the other end of the spectrum, rooting a cutting, grafting a scion, or using tissue culture to reproduce a patented plant is definitely always patent infringement, or providing someone with material for the purpose of doing those things.
If there were a patented plant that produced 100% nucellar embryos in its seeds, there would be a pretty good argument that it would infringe the patent to plant its seeds. However, I'm not aware of any type of mango (or citrus) that
never produces zygotic embryos. Therefore, it seems like you should have the right to plant the seeds even if some percentage of them will be clonal. However, as I said, I think this is an unresolved legal question.
Now if you hypothetically were to figure out which seedlings are clonal and sell them with some kind of statement to that effect, you might be pulling yourself back into infringement land.