Let's assume that the core is made of N-BK7. If we want to account for the Fresnel losses from all air-to-glass interfaces, including at the fiber core, we need to enable the polarization option in the geometric image analysis settings. The polarization calculation will also account for bulk absorption of the bi-convex lens.  

Specify N-BK7 glass at the image surface as fiber core glass material.

Check the “use polarization” option in the geometric image analysis settings.

Click OK.

The new coupling efficiency is about 47%.