FOX and Bilstein both build great quality high end shocks. The shock model used in the TRD Pro is a high level consumer grade shock. Not really in the same category as the model of Fox used in the TRD Pro fox systems. The Fox shocks should be better at everything. Better fast. Better slow. And everything in between.
The reason is that they are multi stage internal bypass shocks, so they have dampening variability through out the range of travel. That opens up a much greater ability to tune for better performance. Better than almost any aftermarket shock for the 4runner. Better than my Fox 2.5's.
The downside of the fox system is that it is location specific. So you can't put taller springs on it without messing up the shock valving. Essentially you can only use a spacer lift on top of the coilover. They are built for that vehicle, with the OEM lift height only. And they *should* be fantastic for that. But they're not going to work well for anything else.
Bilstein also makes some top tier coilovers - but they aren't what's sold in the TRD PRo suspension. The Bilsteins are really comparable to a Fox "adventure" series shock. And the new Fox IBPs are something new. I'm not sure what they're comparable to without having a look at the internals. The next step up for the "adventure" fox shocks are called "performance" series. And the top tier Fox models - that are bolt in coilover kits - are called "Factory" series. They are very similar to "Performance" except they have hardened piston rods that are about 50% harder, use all viton seals, have complex CNC machined pistons, larger more durable reservoir hoses, and other small details that differentiate them. I don't think we really know what comparable product line the new fox shocks fit into. But it's safe to say they are probably equal to the Factory series or maybe better. They are a more complex and advanced shock than any other fox product currently available for the 4runner. The only comparable product I know of in terms of design is the OME BP51.
As an end user - does any of that matter? I think we'll have to drive them back to back to find out. I think the TRD Pro suspension kit now on sale for $500 is a killer deal. You couldn't buy even one Fox front coilover for that and you get all 4 shocks and front springs.
Hope that helps.