To start, one might give this attached study a read. It is fairly introductory and easy to read, and will delve into many mechanisms I am about to discuss:
Basically, there seems to be a phenomenon (perhaps evolution based) that nutrients that co-exist in a plant source seem to work well with other nutrients also found in that plant. This also holds true for animal products. Creatine, CoQ10, Carnitine, and Carnosine all show nutrient synergism with each other, and all are found in meat products and eggs.
This, according to the above article, may be a reason that foods have unpredicted benefits when consumed that are not gained with the isolated compound.
This may be a good rule of thumb to consider when supplementing compounds found in foods. If you have a DIM(Diindoylmethane) supplement, take it with some Brassica vegetables like brocolli. If you have an allicin (garlic extract) compound, take it with a meal that has garlic in it. Polyphenolic mixture? Down it with some fruit. This is a fairly good blanket statement to get the most out of your supplements.
Also, be aware that sometimes supplementation is not needed given you eat the food. And sometimes the food dose is abysmal and supplementation required. It is individual, and would require checking up on the compound in the Examine database or Pubmed/Scirus databases.