Nah, two different BOMs isn't making it more complicated. In the end you hold a board in your hand and have to figure out how to get from it to what you want.

Or think in a different way: A board you have in your hand does not suddenly become more complicated because the company comes up with another board with different BOM. Maybe choosing the board becomes a bit more complicated, maybe choosing any addons for the boards becomes a bit more complicated (as you have to navigate compatibility), but using the board -- I don't think so.