CD is obtained by an integral of the load on all the panels.
The Trefftz version is obtained through an integral on just the trailing edges.
The load on a panel is obtained by summing the loads on the vortex loop edges of the panel. 'Before', the velocities at the edge centers were interpolated from known values. In the version bundled with 3.25.0, this was changed to use velocities directly calculated at the edge centers - this improved accuracy, but is computationally more expensive.
In this version, Dave also recognized that the formulation for the Trefftz analysis was not strictly correct for unsteady cases. I thought he had made another change to fix this, but if it is showing up as zero, I suspect he decided to zero it out when it is not correct. If he can sort out a formulation that works generally, I think it will come back. So long as it is zero, I clearly wouldn't use it.
Yes, in general the Trefftz analysis should match the panel integration version. Yes, it will generally converge before the panel integration version converges.
Rob