You have definitely misunderstood something, as what you are claiming is incorrect.
The system by which the modifications to the tree are determined by the seed has intentionally not been changed since it was introduced, so that the items can continue to function the same way. The Historic jewels actually even have an internal "version" value which was included so that if we ever needed to make such changes, we could have them only apply to new gems and distinguish them in some way by describing the version stat, but we haven't had to actually use that so far.
As noted above, changes to the tree do change the results (and some potential changes to the tree might not be obvious or visible to players, but those would be rare), because the passive skills themselves are inherently one of the inputs. But outside of that, the results of a historic jewel don't change unless it's seed does.
In fact there's a minor bug in the code for making those modifications which...
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