In the current plant patent rules, the patent owners have the full rights and control of asexual propagation of patented cultivars. It specifically stated that propgaation via seed is not covered.

The intent of this law is not to disrupt other plant breeding efforts to develop better cultivars even if the parents are patented. And the law was written a long time ago when lawmakers believed that all seeds are recombined DNA of the parent/s so it would be easy to test propagated materials.

Long after that law was written, scientists found out that some plants including citruses produces nucellar embryos whose DNA are clones of the female parent.

We know that many citruses are nucellar and the seedlings from nucellar seeds would be genetically identical to the female parent patented or not. Case in point is that there are some cultivars in the UCR germplasm that are nucellar origin and we get budwoods from them.

Let us assume for example that we got a seed from the seedless Red Nules, hey, I really wouldn't be surprised at such anomalies that can occur albeit low probability, and the seed happened to have nucellar embryo that sprouted. We then use our acceleration technique of shortening the time of that seedling to mature so that within 2-3 years it is blooming. We then proceeded to asexually propagate them as nucellar Red Nules perhaps using a different name to avoid trademark violation.

Have we done patent infringement? I don't think so but it would be near impossible to differentiate between the original Red Nules and the nucellar Red Nules using genetic testing.

Perhaps you may have read more in details and want to know your interpretation of the most recent plant patent laws.

In Australia the plant variety rights cover commercial propagation.
I dony think that excludes individuals from owning a patented plant, if they can get it.Or does it prevent any own use propagation.
In fact there is a breeders exemption for propagating from patented vars for further research. Generally fruit vars are only released to commercial growers in large numbers, and no nursery will sell you one or two trees. Growers usually sign a licence agreement about the marketing of the fruit from the patented trees, and not re-propagating from them.
If you breed from a patented var, you could patent the results yourself,but the results cannot be genetically identical. There is a threshold of difference that must be obtained, and the plant must clearly be different to the parent in some way.
As i see it, if you obtained seed from red nules, and it turned out to be nucellar ( not always the case ) you can grow it, but if 100% identical, you couldn't commercially propagate or market the fruit.
Similarly you could go back to the original parents of any hybrid var, and perform the same cross, and possibly get something very similar.
If it is too close to the patented var. you may not be able to do much with it.
In the USA, do the plant patent laws actually prevent any individual from owning a plant??

No one in the US can be prevented from owning a patented plant. It covers mostly how they are propagated. It is the patent holders that will enforce plant patent laws.

Future Fruit, LLC devised licensing agreement so that no one else will be propagating the red nules and they concentrated on contract growing for fruit production. Thus the propagation is dramatically simplified so that by logic, anyone producing Red Nules fruits outside of contract growing has surely violated their intellectual property rights. Future Fruit can then prosecute the individual at their own whims or leisure whenever whomever whatever just like the RIAA.

In the real world, some non commercial (private) owner of a Red Nules citrus tree, will of course asexually propagate the tree for their own use, or to give a tree to a friend or relative. Legal or not, this sort of thing has happened with every patented tree in the past, and I assume will continue to be the course in the future. Further, I doubt Future Fruit LLC would bother to pursue a infringement suit against a hobbyist who propagated a second tree for himself, plus I strongly doubt that it would ever come to their attention. - Millet (1,100-)