You'd have to check with your manufacturer to be sure. Very small packages, (0402 is pretty standard now though), "blind" packages (BGA etc), and having lots of different parts (there will be a limit on the number of reels on the pick and place machine) will raise the cost. Tiny and/or blind packages will also reduce your yield.
BOM consolidation allows you to buy more of the same component, taking advantage of bulk cost reduction and also reducing opportunities for incorrect orders. Another factor to consider is that there is always wastage in the pick and place - let's say you lose 10 of each components per run. If you only have 10 BOM lines your overhead is 100 wasted components. If you have 100 BOM lines, your overhead becomes 1000 wasted components.
So, if you get a 10X reduction in cost by reusing a BOM line then do it. If the cost of adding a BOM line is less than reuse, then just add it.