Transistor/gate counts aren't really useful anymore.  There's a saying in the industry "you pay for the wires, we throw in the transistors for free".  Interconnect is everything.  Unfortunately people are seduced by the fact that transistors come in discrete units so you can count how many of them you have.  Interconnect costs are more subtle.

Transistor/gate counts are really only useful if you're comparing standard-cell designs pushed through the same toolchain.  Otherwise the choice of synthesis tool matters way more than the gate count.

It's utterly pointless to compare a standard-cell design to a full-custom design using transistor count.  Even between full-custom designs it's normal to see a 4x variation in area based on the foresight of the architect and the skill of the layout designer.  By the way, BFL doesn't use the phrase "full custom" to mean the same thing it means in the industry.

Also keep in mind that unlike FPGA gates, VLSI gates come in all different sizes.  There are "strong" NAND gates that are 64x (or more) as large as the weakest NAND gates, yet they still count as one gate or four transistors!