Current epidemiology indicates that the concentration of urinary metabolites may ot be the determinant of stone formation. I say this because urinary calcium excretions, as example are widely disparate across the world.
The formation of urinary calculi is a final manifestation of a broad range of etiologies and pathogenesis. A number of chemical and physical factors are known to play their roles.
You are correct. We all have patients who form stones but have normal urinary parameters. Normally this is quoted as only being 3-5% of patients. Thus the current belief is that urinary abnormalities (i.e. excess excretion of calcium, oxalate,uric acid, or low levels of urinary citrate) are the greatest contributers to stone formation in addition to the dietary factors tested in the urine collection. Additional evidence to support this, are the many very good studies demonstrating a decrease in stone formation and recurrence if these urinary abnormalities are corrected either through medications or dietary changes.
That being said, there is likely more to the story of stone formation than just what is abnormal in the 24 hour urine collection. There has been recent research demonstrating that obesity, diabetes, and cardiovascular disease are associated with kidney stone formation. There may be some relationship with systemic inflammation (this is often found in diabetic and pre-diabetic patients). Total dietary calorie intake is may be a risk factor, and this is probably independent of the food patients are eating. Finally exercise and physical activity may be protective against stone formation. None of these factors are "well established" as causative for stone formation, but there certainly are new emerging theories.
Also there are several types of urinary calculi which differ in composition and hence pathogenesis. To date over 200 components have been found in calculi. So there are several reasons for the formation of urinary calculi.