I come from a stone fruit perspective, but we see a similar interactions with the various rootstock choices we have. I believe the expression for the fruiting scion is based on nutrient accumulation of the root, and root size/vigor of the rootstock, which may again be based on nutrient accumulation. With cherries, for example, we always tend to see a smaller root on the less dwarfing rootstocks, but it is not a linear relationship; trees of the same size do not always have the same size roots. Krymsk 5 trees always have a high Manganese content (via sap analysis), substantially higher than any other root we use. They also are more precocious for their vigor. We can push their growth with N fertilization in the first couple years, and then maintain a healthy vigor by cutting it out in subsequent years. I believe this shows the variability of rootstocks reacting to their environment and/or fertilization. If you are assuming you will have a much larger canopy you need to remember that everything is a trade-off. A seedling rootstock may grow quickly, but it may be less efficient in the long term. I believe you need to find a balance, looking for a root that picks up the nutrients to express the genetic potential you desire. Consider something growing 110% of what you need so you have a chance to grow wood for renewal. The restrictions (or as you say “fundamental flaws”) of nutrient accumulation is a positive, not a negative, IF you find the right root for your circumstance.