OpenCL guidelines to use physical pins of fpga

I'm not sure what you're trying to do in your first question, but as far as your second question is concerned, the answer is no. The BSP (the board_spec.xml file you mention) is responsible for configuring the I/O and creating "space" on the FPGA for the kernel hardware, which is created by compiling your kernel code with aoc. You can create OpenCL libraries that include RTL code, but there is no way to add or change the I/O of the device through OpenCL.