Hi Melv.
Here is test for the colliders.
https://www.dropbox.com/s/73itpjgpyh5iofz/ColliderTests.zip?dl=0
Inside, there are 3 scenes :
- 2D collider test
- 3D collider test
- 3D collider with rigidbody test.
In all tests , there are 1000 sprite units just randomly bouncing off the 8 unit world distance. The code to do this is very crude so please ignore my short fall on that one. 
Each unit has collider on it with trigger option turned on and every time it registers OnTriggerEnter event, it will increase a integer value on the Test game object. You can see it on the inspector.
Now after I have done this test, I think I was perhaps prematurely thinking that the only moving part was responsible for the performance difference, but I think the trigger event calculation as well.
2D collider test registers the event against the all other units as well which is perhaps one of the reason why it is more expensive. The 3D collider test without rigidbody only registers event with the one other collider with rigidbody in the middle so a lot less trigger event means it will obviously run faster.
Which is why I tested the 3D collider scene with the units also having the rigidbody. To make everything the same and fair to test. However, interestingly, 3D colliders with rigidbody was still a lot faster than the 2D colliders. Even with units registering events with each other.
The profiler shows that the physics cost is at around 2.5ms or less in average for 3d with rigidbody but for 2D it was at around 7.4ms
This brings up some interesting options.
If I want to create a moving trigger which only tests the event against a static (maybe moving too) , selective and fewer objects then this could be the fastest way to do it. For things like projectiles etc. (without fiddling with physics layers)
The 3d colliders with rigidbody was still a lot faster which is pretty puzzling. Perhaps something about the Collider2D and Rigidbody2D that is very different than the 3D version like you have said is causing the issue. This leaves me to wonder what would be the best practice to do what other 3D collider scene is trying to do. It is obvious to me that I canât be using 1000 units using 2D collider + trigger this way.
The test is running 1000 units, and I am not saying this should be ânormalâ. I perfectly understand that the average need of game may not be that many, and so the application may not be the practical usage. However, I also think it is worth while to notice this performance difference and know the difference and limitation so we can design, work around it to make best use of all.
Perhaps 3D physics runs faster because of Nvidia hardware physx acceleration�
I am here to contribute at any time so please let me know what you think about it. 
Cheers.