Mounting a scope on the barrel is definitley not the ideal way to mount scopes. No doubt. However the main problem with the Encore and Omega is that the front and rear holes are too close together. The mounts need to be "stretched" out a bit.
Personally I would not consider the cheaper Weaver base on my Encore's. I have mounted scopes on well over a dozen different Encore's. However I prefer to use the Warne bases and rings. The Warne bases and rings are longer and stronger.
We have been shooting scopes on MZ's for over 20 years. There are inherent problems with a MZ that you just do not have with a 700 Remington.
When I have used the Warne bases and rings with a good quality scope I do not have any problems with the Encore-or any other MZ for that matter.
Switch to a Warne base-you can still use your Weaver rings. This should take care of your problem. But shimming is definitely not the answer because one person says that Encores have that inherent problem with their barrels. If you continue to have a problem with this then check your scope, or send the barrel back. There definitely is a problem, and the best thing to do is find the problem, and fix it, not put a band-aid on it.
To demonstrate the length difference I have a picture of the Warne vs. the Leupold base. Tom.