Note that a LOT of those transistors are not in the LUTs and FFs but in the routing fabric, there are a lot of fixed at bitstream load time multiplexers involved in routing, and things like the DSP and BRAM cores are not exactly cheap transistor wise either (But much cheaper then building the same things out of generic LUTS and FFs!).
Only a fairly small percentage of the silicon goes on LUTs and user flipflops, most of it is routing and whatever special purpose blocks are appropriate.
Regards, Dan.