Quality Score does play a big role in determining your CPC, however, it isn’t the only factor you need to consider. Your post made no mention of keyword matching options you tried using, nor campaign type.
Keyword matching options make a huge difference in the actual search terms that will trigger your ad impressions. If you were using anything other than exact match keywords you were likely triggering ad impressions for search terms other than the keyword you were targeting. Check the Search Terms Report.
Campaign type is also a factor to consider. If you used the default settings in your campaign (Search Network with Display Select) you would have been targeting both the Search Network and the Display Network. And as you said you were targeting a micro-niche, the bulk of your impressions may have been from the display network, not search.
Even if you had selected Search Network only, the default settings will also include the Search Partner Network, and for some niche products, Search Partners can be the most important network, for both the number of impressions as well as the number of clicks and conversions.
There are many factors to consider when determining where your traffic is coming from and which search terms are actually triggering your ad impressions. You might want to consider taking a look at those individual segments of your reports. You might discover that you are indeed paying much less than you thought for clicks on Google Search for the exact term you were targeting.