Chris,
Like you I have the 2011 (pre model change) Vstrom 650 and last month I was considering exactly the same questions as I have a main stand, side pannier rails, top box rack plus an engine bash plate. I contacted Delkevic, explained my concerns and they were extremely helpful. They confirmed that the fitments on my bike should not cause a problem when fitting one of their systems apart from the bashplate. More research and I found another forum member who commented that he had fitted the bash plate without problem. I then went ahead and ordered from Delkevic and received a well packaged box within two days. I have yet to fit it as I am waiting on the weather being slightly warmer before I commit to a session in my garage. I would add that I did not want a noisy system, just something with a deeper and more characterful sound. It has a removeable baffle if you want more noise. Suggest that you have a look at YouTube as there are a few video posts where you can hear the sound of the new exhaust.