Clearly, everything else neglected, positioning the reinforcement closer to the surface (=further away from the beam axis), increases the effect of the reinforcement and by that the bending resistance.
However, other, frequently stronger, effects can have influence in the opposite direction - among others: corrosion, bond, aggregate size.
To capture these effects in an analysis, one needs a pore flow + chemical analysis for corrosion (or at least some estimate based on the cover depth + type of environment). The rest may be captured by defining the reinforcement bond parameters corresponding to the cover + aggregate size.
In ATENA, with a fine enough mesh for the concrete (usually, mesh size = aggregate size is about the smallest which makes sense), you should be able to get at least a part of the effects even without manually calculating the bond strength reduction.