Yes, the inertia is definitely still there.
My thinking on this was that you can have custom board connected to those gpios and since the IO voltage is adjustable, it might not be configured correctly yet for that expansion board when the bitstream is loaded and so a pullup would be imposing a potentially too high voltage on the external device. OTOH, 100uA is pretty weak so it's doubtful this would cause any damage ...
Another thing that would be useful for the default GPIO config is that ability to configure state change interrupt on them. Not sure if the default EMIO GPIO module allows this (or maybe it's available already in the current config, I haven't checked).