My question is this: is there some way (other than driving slowly so that I can use the n judiciously) to step through code in the debugger, digging down into subroutines if needed, without fear of accidentally stepping into some use'd module? (And no, I cannot use any outside tools. Just Perl and what comes with it.)

You can probably still use DB::Skip (or just crib its code to somewhere that your ~/.perldb can find,) as it doesn't depend on anything else at all except core Perl. I've also shared a bit in Re: Debugging objects as well, feel free to crib what you need.

For a bit of visualizing, I also use ddd to help me find where I am during the step-throughs.