Thank you for replying! After reading carefully, this is my opinion:
Speaking to your point about other recipes: Making the sediment-to-stone recipe generous seems unproblematic and like a good idea to me, because the ingredient is one that belongs to this mod, and there is no energy content to account for. It seems unlikely to cause issues with other mods.
On the other hand, it can be very problematic to apply a large multiplier to an intermediate process that involves items (especially fuel items) from the base game as ingredients. Not only because it breaks energy parity and makes the process ingredient (wood, in this case) a much too efficient carrier of energy, but also because it splits related processes into those that benefit and those that don't, depending on their place in the chain. The change may seem minimal or carefully targeted, but it actually has significant side effects in relation to mods that provide their own (often balanced!) means of producing wood or converting it into coal and other materials (such as oil). Applying the bonus right at the stage of resource production instead of later, ensures consistency across the process chains and generally pre-empts the need to rebalance such mods specifically for this one. It resolves the issues with energy parity and density at the same time.
Applying an energy bonus factor of 20x seems fundamentally very sensible to me, not only because it makes the challenge less tedious, but because the energy output of Yumako trees and Jellystems already is greater than that of normal trees, by a factor of 25x and 62.5x, respectively. It seems to me that, here is an excellent opportunity to more directly "fix" some of that disparity of Space Age, by just making the trees of Nauvis 80% as productive as Yumako trees. (It seems even more fair when you consider that Nauvis receives twice the amount of sunlight that Gleba does...)
So I still think that only modifying the yield of trees is the better option, but you seem to worry about "messing with trees". What do you figure is the problem with that, if you don't mind my asking? It seems simple enough to change the parameters, if it is only for the growable tree.
Anyway, I hope that you at least find my thoughts useful!