Bad engineering or attempted subterfuge?
Well, sometimes it is easier to route the traces for a board if you can re-assign the pins on a device. The pin order on the sideport for these signals is in a pretty crazy order. That said, doing it on purpose to something like an eprom that requires a contract with another device, is evil. If their goal was subterfuge, then it was clever. If their goal was to save a batch of pcboards that were designed wrong, then it was resourceful. If their goal was to just be easier, then I'd call it lazy, but that is me being judgmental, without any knowledge of 1980s EDA tools.
I just did this on my TIPI project, but that was a MISTAKE. Not intentional, will be corrected before release.