Based on my understanding, the small scale culture can provide the characteristic spectral signals for the representative metabolites in the fermentation. The large scale fermentation can enrich the metabolites. So they can be isolated and identified, especially for the trace metabolites. Small scale is energy and time saving. We can choose which fungus to do the large scale fermentation based on their small scale spectral signal. However, there will be a difference between the metabolites in small scale and large scale, if you take the quorum sensing in consideration. So the conditions in large scale fermentation are also very important. Hope this helps.

A good response by @Shasha Hu.

In addition, I feel that the primary purpose of a small scale production is the verification of laboratory procedures and their modification before engaging in large scale. Some of the benefits include minimize manual handling and economic on scale. They also help the researcher to adjust key variable before a move to large scale

Large scale fermentations are utilized to produce massive quantities of secondary metabolites by selected fungi. Large scale experimentation are time consuming and expensive, which is why the small scale is necessary (especially, in the case of novel study).

In summary, the small scale endophytic fungi culture allows for the preliminary screening of numerous fungal extracts for desired bioactivities or products. From which the best performers can be selected for large scale to further the study, increase the scope and characterize the compounds produced.

Good luck !