I think that the increase of secondary metabolites in MPs, while intercropping is related to competinion between plants. Secondary metabolites are very often produced to gain a upper hand over the rival/vermin etc. While intercropping MP is less "relaxed" and needs to secure it safety.
Of course, one has to be careful while choosing crops intended for intercropping, since wrong matching may decrease the MPs growth/secondary metabolites production efficiency and so on.
Probably, this is not an only reason of increased secondary metabolites production in this situation, but someone more specialized in this area should share his opinion.
Any inter-crop in medicinal plants cultivation leads to the competition of the medicinal plants with the inter-crop. This competition may be for light, space and nutrition. During this competition, medicinal may face more stress which may ultimately lead to the improved production of secondary metabolites.