Regarding the question about bitstream compatibility, the answer is no, a bitstream built for VCU1525 will not work on the XUPP3R. The clock & USB UART are on different pins, so I must 'build' two versions of the bitstream, one for each card. Although the change in the code is tiny, it still takes the tools 5+ hours to re-run place & route, with multiple runs needed to get a success.
Can you inplement a double set of interfaces to support both boards by the single firmware?
BUFGMUX_CTRL can be used to select the clock signal, if clocking assignment is different.
It is probably possible to build one firmware for both board.