I remember hearing or reading the routine use of the appraisal waiver form should be avoided, this seems to be something our commercial loan department has been doing regularly (using the waiver), but is this specifically addressed somewhere (to not make it a regular practice of using the appraisal waiver form)? Thanks.

Here's a thread that discusses the waiver issue:
Waiver Discussion

Although the rule doesn't specifically prohibit the practice, commentary in the preamble suggests the waivers should be infrequent, and most likely not within the spirit of the rule. Examiners appear to be asking what the bank's practice is, but haven't heard if examiners are actually citing the practice of routinely offering an option to waive the 3-day prior receipt of appraisal as a violation.

To me, routine use of a waiver means that the bank expects to always be receiving appraisals late in the process. To which I would have to ask, "Why? Aren't you ordering them on a timely basis?"

Tagging on: 2 purchase loans closing simultaneously; LTV ratio required a different property to be taken as additional collateral for both loans: taking a 1st lien with one loan, subordinate lien with the other. Appraisals for the two purchase properties were received weeks ago. Appraisal for the extra collateral property will only be received within a few days of closing. Use the waiver (for the additional property) or (we document delivery by using an acknowledgment of receipt form) use the acknowledgment, based on the purchase property's appraisal?

You would need a waiver signed prior to three days before closing to deliver late. An acknowledgement won't get you anything except agreement that you were late.