The very simple answer to your question is "Yes". There is a vast amount of secondary metabolites out there, which has not been identified or tested yet. Lead compounds are not limited to alkaloids, one of the important pain killers, still today, is salicylic acid, and this is not an alkaloid. 

However, there are probably differences in how often alkaloids come out positive in various tests versus flavonoids. If a secondary metabolite is ingested daily, e.g. a flavonoid like quercetin, which is found in the peel of many fruits and vegetables, we would probably have noticed the beneficial effects of this compound - but you never know and it may just be that the no one have tested quercetin for the right effects yet. 

Lead compounds could mean compounds that are specific for a particular species, e.g. paclitaxel in Taxus brevifolia, compounds that are easily detectable and analytically prominent such as chlorogenic acid, compounds that account for properties of interest such capsaicinoids in Capsicum spp., or compounds that represent a large portion of the soluble substance such as rutin in Fagopyrum.

 lead compounds are many and specific to the species. what u mentioned are 2 types of broad class of chemicals found in the plants. the primary and secondary metabolites are many more. the starch is lead compoud in rice, wheat,potato is carbohydrates. but there are also minerals, vitamins, present in same also lead compounds when they are viewed for nutrients. so in your statement it should be very c lear to that, lead compounds pertaining to therapeuctis means secondary metabolites like alkaloids, flavonoids, phenols, glycosides, isoprenes, terpenoids, steroids etc. for better understanding plz read any book on PHARMACOGNOSY gives u better understanding about the chemistry of natural products. all the best.

every plant spices contained unique compounds, as citrus have vitamin C and flavonoids (Naringine), parsley have apignin, basil volatile oil have linalool, spearmint have manitol etc