Good news! I took it apart, and as you guys noticed, it was indeed "upside down". So I inverted it (skinny 30mm end towards the top, and fat 35mm end towards the bottom with the hard plastic cap). With no pressure at all on the ti link, it does indeed appear to be a few mm ahead of the suspension centreline. However, I adjusted the position of the suspension cap by screwing it down a bit further so the elastomer is pushed out more than before. What that does is that it pushes the ti link further down to the point that the suspension spike lines up with the central groove on the ti link plate. At first the ti link adopted a bit of an S-shape (see picture), but after tightening everything back it seems less noticeable now and pretty much straight.
(bike is standing up with the front wheel and pedals on the ground)
FYI, the elastomer is now protruding about 20mm or so from the frame. The pic was before I put my weight on it though, so it may have compressed/settled into the grooved plate a bit more.
Now, the alignment seems better than before. I wouldn't say it's perfect but it's way less uneven than before and is only visible upon very careful inspection.
Jeremy, the carbon fiber stay looks straight, though I didn't measure it. Looking at pictures of other Silvios, they do seem to have a very slight bend in the rear half. I'll see if I can measure the difference tomorrow.
Thanks again, all your input was very useful and appreciated! Looking forward to the next 6-8 weeks before the season ends and the chilly Montreal winter sets in..