With the c_trace function you're able to do any collision system you can imagine on your own. So you've got the engines ellispoid collision system, the PhysX collision system plus the ability to implement any system you like. If you use PhysX you've got a complete physics simulation system, taking away a lot of these time consuming and complex tasks for you. Hence the level of control you have is reduced by this system. This is not a flaw but a necessary consequence of the system design.

Under the line you still have all possibilities to realize any collision you like. And I highly recommend not to see JCL as a problem. He is a very clever and intelligent person and he succeded to adapting this engine from the 90s up to today. That includes doing some pretty hard decisions and even choosing which feature to implement and which feature to abandon.