Yes that is exactly right. In certain species that exhibited undesirable floral phyllotaxy, like in tomatoes that did not fruit, some extra auxin was added to just the apex (the growing tip) and this caused the desired pattern to be re-established, and they got the tomatoes back. This is largely how we know that auxin concentrations in the apex (the peripheral zone) are important to a lot of species. As you say, this is not always the case because some species are genetically-predisposed, there are other environmental factors, and there can be a mutation, etc. There is also considerable evolutionary diversity with how auxins are managed by different plants, like you mention. We can expect many plants to actively manage auxin to advantage their growth, as you put it.
To make matters even more complex, both the roots and the growing tips are dependent upon auxin, and if you cut and release auxin into the aquarium water column, then firstly you will loose some auxin from the plant phloem, and secondly, auxin will enter into the water column and potentially be
reabsorbed by the plants, meaning that the concentrations could be less likely to remain stable in the fist place. Auxin is a commonly called a "stress response" hormone, so it is not unimaginable to think that the changes could be induced by cutting and replanting. But there are so many strong variables, this is complete conjecture on my part, and is very much on the dark side of the moon in terms of what people actually believe.
Auxin moves in a complex with PIN1 proteins when it leaves the source cell (auxin efflux) and will travel both through both plant cellular tissue and through vascular tissue (notably the phloem). It seems to do this due to polarity and pH gradients within the plant. Unfortunately, it only gets more complex and we have to looks at some very immersive biochemistry to understand this fully. But this webpage has a
fairly simple description that might help if somebody was interested. The best way to look at it is through the
chemiosomotic model, developed by some very forward-thinking
individuals. But ultimately, you don't need to know any of this really.
Exactly right again! It is also rather possible that this could have been triggered due to environmental conditions like high light and air exchange levels, because I faintly remember that
R wallichii can have a spiralling phyllotactic pattern when emergent and terrestrial. There is absolutely no certainty that I know what is going on or what could happen. Many scientists are still chipping away at these topics. There is overwhelming uncertainty unless the species has been studied before.