When scoping an Encore the bell diameter is an issue, but not a big issue. The big issue when mounting a scope on an Encore is the length of the scope, and the size of the eyepiece.
For simple reasons. First the D&T'd holes in an Encore barrel are pretty close together. So I try to buy a longer scope base. This allows for more adjustment(fore and aft) of the scope. Then you need to remember that the Encore has a hammer that sits fairly high. So fore and aft adjustment is important to clear the hammer.
So just saying 3X9X40 is not enough information. Is it a short compact, or a long scope. Does it have a large adjustment ring, or is it built in?? And are you using short bases or long bases.
I use a long base with a fairly long scope with good adjustment on mine. And a built in power ring. So I can get away with low rings on my Encore. Your results may vary.
Below is a picture comparing the length of the Leupold base to the Warne base for an Encore. I much prefer the Warne. Tom.