Here is a good article on how the stock damper works.
As far as keeping it on or taking it off. I have a Scotts and the Honda HPSD on a 2008 450X. I have the sweep set to 34 degrees range and the high speed set to where there is just a little noticable drag on the Scotts and the Honda one set to max damp.
You can change the wt of the oil inside the HPSD and the 450R model has stiffer spring you can buy or shim the stock spring, but I would not do it over again myself.
Before I put the Scotts on I have tried everything I could to make the HPSD work a little better but no matter what we tried it made so little difference you could not even tell.
As for the two fighting each other. I have my sweep set narrow on the Scotts so it is about finished where the HPSD pretends to do it's thing. I tested with the sweep at its widest setting making it dampen from lock to lock and it would mask the HPSD to where you did not even know it existed. Leave it on, take it off doubt you would even notice.
I already had the Scotts unit when I got this 08 so I used it, but there are some better dampers out there.
I ride an 450X woods/cross country and this is only my opinion, but I hope it saves someone a little effort.