You are free to use the design any way you choose. It is open source. As to the BeagleBone Black itself, we are not here to supply thousands of board to be sucked up in companies as is the case with other boards so they can show inflated sales numbers. For a more detailed explanation, go here.
BBB has no onboard JTAG for you to use. I have no objections to you looking at the following link for a description of the product and background information on it.
Sorry but on the onboard DDR, you have no choice but to use it. Otherwise the processor cannot function without it.
eMMC does occupy some of the GPMC bus. Even the LCD occupies some of the GPMC bus. If you need to use the same pins as the eMMC for these GPMC functions, then no you cannot use them both at the same time.