There is a caveat here in that these masses are large enough to make the Earth’s acceleration significant, and the Earth’s acceleration is not the same in the two cases. There is no problem dealing with that, but I think that just clouds your issue (particularly if you don’t like math) and we should stick with comparing bowling balls and feathers so we can ignore the Earth’s response.
To be fair (I almost hate to do this) I think I’ll have to explain. To be more precise, at the moment the two cases are at the same distance from the Earth they both experience the same acceleration (relative to the fixed stars, say). As described in previous posts, both the Force and the inertia are proportional to mass and the mass cancels. So, in that sense, they do not fall at different rates.
However, the Earth is also being pulled and has its own significant acceleration. The Earth’s acceleration is different in the two cases, so Mercury would get to the Earth sooner. So in that sense you could say it falls faster.
Or, to put it another way, in center of mass coordinates the acceleration of the second mass is not independent of the second mass. However, the dependence is $$ \left( \frac {m_1} {m_1 + m_2} \right) ^2 $$ so when m1 is significantly greater than m2 this quickly becomes 1.