The part that's confusing you is safe withdrawal rate (SWR) and actual withdrawal rate.
In the OP, you were saying if you decreased withdrawals to 3%, the total portfolio requirement should go down. This is actually true. If you had a $1 million stash and you were withdrawing 3% instead of 4%, that $1 million would be overkill and your total amount should decrease ($30,000 instead of $40,000)
What the calculator is doing, however, is the safe withdrawal rate. It's saying if you were to withdraw 4% of your portfolio indefinitely, it would never run out with spending being a constant number ($40,000 on a $1 million portfolio). If your required spending doesn't change (i.e. it's still $40,000), it's assuming that it is now 3% of your portfolio balance which gives you a higher total portfolio balance ($1.3M).
I think the answer what you thought it'd be doing, you'd decrease total withdrawals to $30,000 and end up needing a 4% SWR on a portfolio of $750,000 (insert your own numbers obviously).