Bed Puddles?

Nope! It's been that way since the 2005 MY.

Look under you're rear fender. Composite bolted to the frame.

 

So I won't connect with steel if I drill the holes larger?

Because I live in constant fear of rust. Had a bad rust experience.

 

Just be careful when the drill goes through the bed. Make you you don't hit anything underneath.

 

nope. no steel beneath the bed.
Not a super detailed view, but here ya go: https://www.youtube.com/watch?v=8aesr9D8V6I

Also, I have a tonneau cover with holes drilled for drainage. similar to this: https://www.tacomaworld.com/threads/bakflip-tonneau-covers-drill-drain-holes.439683/