why do we do this, what are the benefits, and does it make troubleshooting down the road more difficult?

In my new job, one of the jm doesn't explain too many things...

there were 2 3-ways in a 2gang. old wiring with the paper... the neutrals were hots, and there was a red from one and a white from the other merretted together loose in the box. Where was the switch leg??