"instead of them receiving a blank form from the IRS to fill out manually."

And the form instructions tell you that if it didn't come with some of your info filled in by the IRS, you fill it in.

"As I said in my initial post, this is the first client I've had who received the 433-D after filing a Form 9465 for an Installment Agreement Request. So, why are some set up directly from the 9465, while other are done using a 433-D?"

Because it has to do with the Payment. This is what I put last week: "This form allows the IRS to set up automatic payments with a taxpayer. ... It affords the taxpayer a lower user fee than a regular agreement."

And you see what I copied here are links for various ways to make the payment.

There are various fees and costs for the process of getting and fulfilling the installment process. This happens to be one of them.

"by filling out that form using ProSeries and print it for them to sign and send."

Okay, let's try it like this: Think of a Bank. You set up payment Terms, amounts, frequency of withdrawal, and how much to be taken each time, with the bank by ACH. That's the same concept as this form. They are signing up for the Payment processing. It's not an income tax issue, now. It's a Liability issue, now.

Every link I gave you goes somewhere different, and if you really want to do a deep dive on this, you can see all the different costs, and how some of them can be waived or the  client can apply to have them waived, or use a different payment method to reduce fees, or apply online vs paper, or fax instead of mail. All of this is like a menu. That's why it is all in different places, with lots of links, for IRS.