Just like they did with PS2, by leaving T&L out of the GS, their "vertex shaders" (the VUs) run at 300MHz instead of 150MHz. Without considering the fact that they were also much more interesting units than Vertex Shaders themselves.
I think PS2's design philosophy was a bit different. Back in those console days the CPU still did the TnL. Also the GS with all that eDRAM was already a big chip so it would've been inmpossible to add on a TnL unit that's why in the end you had the VUs on the EE.