Whoa boy, do I have stories. Short answer: do their work for them. Have a list of nearby recent comps, provide a list of upgrades, try to get a local appraiser.
Here's an example on a rental property: I couldn't be there, so I spoke to the appraiser on the phone in advance. Since I was an original owner in the development, I was able to point out added features (extended garage, extended casita, oversized lot, gourmet kitchen package, etc.). I also gave her tips on how to identify those upgrades on any property in the 5,000 home development and what these upgrades cost when the homes were built. The result? The appraiser used choice comps and the number came in insanely high. I was just doing a re-fi, and didn't plan to sell, so as long as it hit the LTV I needed, I was happy. At the time, there were several distressed property sales as comps, so it was time very well spent.
Our primary home was a short sale, partly because it was overbuilt for the area. (We didn't care, because it fit our family's needs + walk to work for DH.) It came on the market in 2012 for $800k. The lender only wanted to see the highest and best offer; we had to bid $928k to be that. We didn't care about the appraisal because we knew the house and we were paying cash. The short sale lender cared quite a bit as the owner/builder was underwater. Their appraisal indicated that the house was worth $35k more than our offer and they tried to strongarm us for it. Our Realtor fought like a tiger for us. She couldn't get them to replace the distant appraiser, but she picked apart his comps and provided them with a list of better ones. Eventually, the lender backed down and accepted our offer as written. Luckily, this was before the market exploded. Nine years later, the value exceeds our wildest expectation.
Based on these and other experiences, my advice is to fight. I'd probably start by verifying that the appraiser is experienced with multifamily and/or commercial property. If this means choosing another lender, there's your answer.
Best of luck to you!
Oh, I just remembered that Zillow has a fun tool for comps. Look up your property, "Claim" it as the owner, and they will show you the comps they used. You can challenge those comps, and Zillow will show you more. Do this until you find closer matches and save them. I did this several years ago. To this day, Zillow's Zestimate closely reflects the current market. Redfin is consistently over $300k lower.
One more thought. My parent's 5BR, 3 bath, 2 story house showed up as 1328 sf on MLS. I called the Tax Assassin's (<--- auto carrot) office, and they blamed the builder's original inputs and said they'd look into it. I used the Zillow feature described above to correct the number. Just yesterday, I was surfing the old neighborhood. I noticed Zillow reported "Other interior features - Total interior livable area: 2,149 sqft" for my parent's house and two others of the same floor plan, which is correct. However, all the rest of this plan in the development still have the wrong numbers. Relevance: check to see what stats the Tax Assessor's office is using. Ha! I just remembered (again) the same thing happened on the rental I mentioned above because of the optional extended casita. Same process fixed it.