Hi, quick update for those who might have this problem later. I've managed to solve this issue (well, generate a bitstream, not sure if it really works yet) by checking in the digilent boards folder from here. In the "Nexys4 DDR" folder there is a file named "part0_pins.xml". In this you will find what is used to generate the .xdc file from the Block Design for the SD slot.
<pin index="171" name ="SD1" iostandard="LVCMOS33" loc="D2"/>
And from this you write lines in this format in a constraint file that you can create if needed to tell to your wrapper which pin you assign to which pin of the FPGA.
set_property -dict {PACKAGE_PIN D2 IOSTANDARD LVCMOS33} [get_ports sd_pin1_io]
And in the Block Design, double click the PModSD block and set the "Board Parameter" to "Custom" to tell the software that you don't want it to generate an automated constraint file for this block.
I've not yet tried to do a software test to be sure that this trick indeed solved my issue since I've some other issues with petalinux and the SD card (obvious incompatible drivers from the PModSD drivers) but that might be a hint for your own work.