Assuming a woody plant naturally has a valuable compound, say a kind of sterol. During an RNA-seq analysis, almost all genes involved in the biosynthesis pathway of this sterol were identified in the plant. I was wondering what are the benefits of this finding? If this study was done in a bacterium or fungus instead of a plant, the importance of this finding is clearer, at least for me, since these simple organisms can be the factory of valuable compounds by genetic engineering technology. But, what about a woody plant which cannot be engineered and grown in bulk?
You essentially gave the answer in your question. By identifying the biosynthetic pathway(s) required to create the compound in the plant, its natural host, those genes can then be cloned and transferred into an expression system like bacteria, yeast, or other plant cells like Arabidopsis thaliana to generate larger quantities of the compound of interest than would be possible from harvesting and processing the original plant itself.