The TRD is made by aFe. Besides minor cosmetic differences (red vs. black hoses, TRD vs. aFe logos) they are pretty much the same except 2 things:
1) The aFe has a big hole on the front bottom of the intake box which is there to help it breathe better overall, and possibly drain any water in the intake box. aFe sells a 'plug' that covers this hole, or you could tape it up.
2) The price. The TRD is more expensive than the aFe
Here is a side by side comparison of the entire CAI system:
Pictured at the top is the aFe CAI system with the ProDry-S filter. This is the 'everyday' filter that is maintained by tapping away debris/dust and can be washed but does NOT have to be oiled (aFe sells a ProGuard-7 which needs to be oiled). Below that is the TRD CAI system with the TRD filter. This filter must be maintained by tapping away debris/dust , washed, and needs to be oiled.
Side by side of the intake box:
As you can see, there is a lower area with a hole on the aFe
The aFe intake box filter-to-body opening measurements on the left measures the same (4.25") as the TRD on the right. I did notice a subtle difference in the 3 hex bolts that keep them in place.
The 'trumpet' wide-mouth of the air inlet is also the same measurements (5.5"W-4.25"H). The aFe is on the left, TRD on the right.
This is the boxes upside down. The aFe on left is distinguised by the buldge from the opening compared to the TRD on the right. They use the same 3 points for mounting the box to the engine bay.
Side by side of the intake neck:
Instead of showing you guys redundant measurements of ALL the openings I decided to just take a picture of them. They are exactly the same.
I wasn't too shocked that they were EXACTLY the same in most aspects. Everyone said this but I never saw a side-by-side comparison. What did shock me was the red hoses that come with the TRD had this stamped on it: