It is very appropriate for an appraiser at any level to question everything. Trusting is okay, but also verify to make sure it applies to the situation at hand. When you sign on the dotted line, you are responsible for your own opinion and you shouldn't be forced to adopt anybody else's opinion. If a co-signing and supervisory appraiser is doing things you cannot reconcile with, there's nothing wrong with letting them single-sign it and then include the appropriate disclosures that you worked on the assignment. It shouldn't cause any problems.
For quantitative adjustments, I generally compare all my sales data against each other, including the sales I don't present in the report. Prior to making any adjustments, the data should represent be a general range in values that will narrow considerably as you sift through it and discard the ones that are less directly comparable. When you finally get down to your "best" comparables (as in, most similar, not highest value) the range should already be relatively tight depending on how similar they really are. By this time you should be getting a pretty good idea which elements are of effect on value within that market segment and where it's trending. There should be no one sale that makes or breaks an appraisal because if there is, there's a pretty good bet that that one sale doesn't represent the trend.
If there is no apparent support among your sales data for an adjustment, sometimes it's best to simply note the difference but otherwise leave the data alone. Better to do that than make an adjustment that you can't explain or support. I find this happens sometimes when comparing homes in some market segments with and without pools, for instance. Or four bedroom vs. three bedroom homes. Or properties with elevated lots and a minor view amenity vs. more level, but non-view sites. Of course, it's always best to find at least 3 of a kind when you're looking at homes with pools or 4th bedrooms or views, but sometimes you have to take what you can get and work with what you have.
If nothing else, you should also get into the habit of ranking your comparable sales in relation to your subject, both before and after any adjustments. Go for the demonstrated trend rather than the outliners and you almost can't go wrong.