We could not say if the appraisal is "low" or simply lower than desired. One can put in a lot of upgrades that do not equal an increase in value. For instance, often mechanical updates simply bring the house up to code. Buyers expect a furnace to work and windows to keep out the elements, and a roof not to leak. Those repairs are maintenance issues and often do not get anywhere near the cost in return on investment. Cosmetics tend to have more bang for the buck, but at the same time, could be non-starters as well.
Something I am seeing right now in my neighborhood is that condominium units that are fully upgraded/updated, set the higher prices, and the dated units are priced almost at the same price and then sell due to lack of inventory. For flippers to make money, the key is the buy, getting a really good deal, and then to not overdo it on the remodel. As a MCM, there may have been a lot of appeal in the original condition as well, in particular if there were some really stunning tilework replaced with modern stuff that ends up dated next season. Those barn doors (not saying that is what you have) are starting to become passe as well.
HGTV has changed residential real estate trends in many areas.
With regard to your situation, talk with the lender and find out why this is not something that can be looked at? Appraisers are humans (for now) and can have errors, but if the appraisal is well supported, the lender will tell you so and why, if it is something that is difficult to figure out on your own (as you are the consumer, not the intended user of the report, and it was developed and written for the appraisers client, the lender).
Finally, for a final inspection, the appraiser needs to go out and look for themself.
