I have a 2004 T100. I got a set of Thruxton silencers but they wouldn't work with the Bonneville headers without bending the Bonneville headers. A couple of years later I got a set of used Thruxton headers and was finally able to bolt them on. So, in my experience, Thruxton silencers require Thruxton headers, but if you have both Thruxton headers and silencers, they will bolt right on.
The only problem I had is the T100 side stand hits the cans in when in the up position. To resolve, I fabbed up a little metal tab that bolts on using the same bolt that attaches the cans to the headers. So now, the side stand hits my little metal tab instead of the shiny chrome cans. I can post a pick if anyone wants to see it.