@jpeyron After two weeks of fiddling, my project partner and I got your block diagram project to work! We did so by eliminating any discrepancies we could find between the implemented schematic from your block diagram with the implemented schematic of from the top file.
Specifically we made the following changes:
1.) Used the pynq-z1 board file from here.
2.) I changed the i2c interface you outlined to the one specified in the top file of the project from github.
The end result was that I got a schematic in the implemented design which exactly matched the schematic generated from the top file.
Thank you for your time and efforts! I'm sure I'll be back with more questions later.