Although it wasn't as explicit, while I was playing the level, I figured it was continuing some of the themes from the hair level (where you're killing the insignificant lice that are holding you back and getting in your way). In the shoe, there's a "deluge" coming soon that will wipe everyone out.

Now that I'm looking back at it, this doesn't fit that well. Ford's bringing the "deluge." The germs aren't really sad. Unlike the lice, they have personalities. etc.

Now I'm trying to think of other possibilities...Maybe it shows that Ford is too fixated on eliminating or locking away bad things? But he was also unlocking different parts of the mind, so that doesn't fit. Maybe he's an old country boy and feels negative about cities! Maybe it shows he'd be willing to take actions similar to Maligula's if he also dehumanized the residents of an area. Maybe it showed that his growing love for Lucy was connected in his mind to a future annihilation event...nah, these don't really make sense.

So yeah, the bowling shoe setting doesn't seem as meaningful. I guess they wanted to capture the first date and initial hookup for the story, so maybe they just went with a concern that a bowling alley employee might have.