Yep it can trap dirt and moisture. The hole stamped in the floor pan for the four speed cars is smaller than the outside flange of the hump. If you place the hump on the pan, it will drop right into place. Take a sharpie marker and trace around the outside of the flange. I removed a hump from a parts car (back before there were reproductions) and the measurements I took were something like 1" from outside flange up towards the firewall and back by lower end of hole next to the seat. The rest (flat floor area and top of hump seemed to be about 1-1/4" to 1-1/2" away from outside flange. To make sure you have enough space, I'd go with the 1". The rods up at the front get pretty close to the floor.

Here is a worms eye view looking up at shifter. You can see floor pan is close to rods. I actually shipped paint when installing the assembled trans when I restored the car. I now pull shifter and linkage. Where the paint is chipped is a little shelf of the floor pan. Could probably place a dime or so up there. It should have been cut a bit more. The donor hump came from a rusted floor pan so was hard to get good measurements. From the factory all this work was done as the body was being assembled and the whole thing got dipped and primed. So the potential to rust was about the same as other places on the body.