It sounds like this appraisal didn't include an income approach. In and of itself that isn't necessarily a problem as far as valuing your property because the dominant approach to value for 3-unit properties may be Sales Comparison anyway.
The difficulty in comparing multi-family properties to each other is that - in many areas - the unit mix (how many 1bd, how many 2bd, how many 3bd) varies greatly among such properties. It can get tricky trying to figure out exactly how much contributory value there is in an extra bedroom or an extra unit, particularly when there aren't a lot of sales data to work with in the first place.
If the appraisal company hasn't already figured this out, one way to account for the difference in location between your property vs the sales in town may be to compare rents (AFTER consideration of your inclusion of all utilities in your rents). In other words, the first step would be in figuring out how much those owner-paid utilities are actually costing and extracting them out of the rent to render that rental basis similar to how other units are being rented in the market.
After the utilities adjustment, a straight up comparison should demonstrate whether the rental basis in your area is higher, lower, or similar to the rents elsewhere. If it's the same then there may not be an adjustment to make for location. If your rents are lower then that could support a downward adjustment to your unit values based on the location.
For the sake of simplicity, let's assume you have (3) 2bd units, each of which would rent for $800/month if the tenants were paying their own utilities. Everything else being equal, if the units in town were renting for $880/month (10% more), then that could support adjusting their sale prices down by 10% to "make" them equal to your units. Presumably that 10% premium would be attributed to the location.
Another way to compare for location influences (albeit more indirect) is to compare the sale prices of otherwise similar homes in the two areas. If a home in town costs 10% more than the same home in your area that difference could also be argued to apply to the comparison of 3-unit properties, too. Maybe.
Working with small sets of data can sometimes get tricky. But that's no excuse for not making an effort to at least consider the effect on value of the location when compared to sales data from outside the area. That's a fundamental. Regardless if the appraiser agreed with you or not they should already have had an answer at the tip of their tongue for your question of whether or not they considered the difference in location in their analysis. An appraiser cannot can't get to a value conclusion without fully understanding how they got there.