how to bypass IO limit to get a utilization summary?

I've no experience with such a large design, but for smaller ones I make pins virtual by prepending 'v_' to all relevant pins and use the Assignment Editor to add a 'Virtual pin' assignment to 'v_*' pins.

Don't create entities grouping I/O: the compiler will use depencies on the few pins that remain to to synthesize large parts of the design away. Virtual pins tell it not to have any assumptions about the signal on that pin.