The Package files from other products/affect inventory setting does just that: it sends a link for another product's file and/or affects another product's in-stock inventory figure.
If you don't need to do either of those things, then you don't need to use any special setting to create a product bundle; you just create a new product that consists of whatever you wish. E.g., if you have Product A and Product B, you can simply create a Product C that you understand to be equivalent to ordering A and B together, without having to use any special setting.
