To your first point, I can tell you my experience is that most bankers for non-sale loans generally believe appraisers are misrepresenting values with a lower bias to reduce liability. Personally, I do not agree with either your logic or theirs; the appraiser expresses an opinion based on their view of the market outside the boundaries of a preconceived notion of value.
I am just telling you what most risk people I know believe. I am guessing that the "bankers" who think otherwise are on the origination/sales side of the business. I will say that the internal studies we did on this issue at my company indicate that the there is an upward appraisal bias estimated at 2-2.5% for purchase related appraisals and 3.5-4% for refinance related appraisals
To your second point regarding the development of adjustments, I agree it would be great if there were a way to efficiently develop a regression analysis on each particular criterion of adjustment; however, the ability to obtain the necessary data so that such a regression were reliable is a fantasy. To wit, how does a regression analysis account for differences in quality or condition? Functional utility? Does a quick deed sale automatically call for a sale condition adjustment because it's not a warranty deed?
Although gathering enough data in rural areas is tough, in many suburban and urban areas, there is more than enough data to perform a very robust regression analysis and it is actually extremely easy in a lot of MLS systems to download data in a a format that is useable in a spreadsheet without that much difficulty. You will never have 100% of the data that you may like, but the beauty of using a regression analysis is that by analyzing a large dataset, you can overcome the lack of certain data. For instance, say you want to estimate the value of additional sf in the GLA...if you analyze a large enough dataset, you will be able to derive a credible estimate even if you do not have data regarding the condition and quality of the homes
To your last point, and based on what I have seen so far, I agree that on a general basis, appraisers need to make sure that they are providing a clear picture of the environment in which the subject property lies, and need to provide more detailed language on how adjustments are developed. There are a number of reports I have seen where the vagueness of language makes me cringe, and the adjustments used by the appraiser might have well come from a Zoltan the Magnificent arcade machine.