It depends which way the taper goes -- is the front of the base higher or lower than the back. I do not have sensitive enough tools to tell whether the issue is this, or something that happens because as I stated the two sets of screws are unusually far back on the base.

As the OP indicated, when mounted the front of the scope base is slightly separated from the barrel. It is not hard to imagine, then, why the gun is shooting low if indeed the entire mounting surface is parallel to the bore (it is nothing more than an assumption to say that since there is a gap as the barrel tapers that the base must be parallel to the bore). Shimming the back removes this gap and fixes the problem, more or less. At least, for the 4 guns I have had personal hands-on experience fixing. So, for some reason, the entire mounting surface is not flat and parallel to the bore. The base ends up pointing slightly up. If you are so curious as to the "mysterious" properties of T/C barrels I suggest you get a micrometer and figure out the EXACT cause for yourself and us all.

To insinuate it can't be the barrel because similarly designed CVA guns don't have this problem is a bit silly, isn't it? The barrels are made by different companies to different specifications -- they are similar in cosmetics only. Does CVA use the same screw mounting system? That is like saying a Remington 700 can't have a certain problem because a Winchester Model 70 doesn't have it. C'mon now...