I'll use the atmosphere as my big natural lens. So I'll watch the upcoming mercury transit at the sunset time where the sun looks bigger than usual.
While the Sun and Moon might seem larger at the horizon, their angular size doesn't get larger. It's an optical illusion.
Will this make the black dot of mercury bigger or big enough to be obviously seen by the naked eye?
Therefore, no it won't, and never ever look directly at the Sun unless you are using appropriate Eclipse-viewing glasses that are specifically designed for this purpose. Sunglasses are not the correct thing to use, they can block some wavelengths more than others, causing your pupils to dilate while still passing some damaging wavelengths.
Properly protected human vision - No.
At closest approach, mercury is only 11 arcseconds wide, well below what we can resolve with unaided vision. We can still notice stars because they are on a black background, but it doesn't work the other way around. Mercury's sub-resolution black spot would not be noticeable against a bright disk.
Pinhole projector (aka camera obscura) - No.
In this Astronomy SE answer I've said that even using a pinhole projector, you won't be able to see Mercury's transit since they provide very low resolution.