I have a site with about 20k pages indexed in google, it has a sitewide link to another site of mine and that site only shows like 10% of those links in webmaster tools. These would all show up if webmaster tools was showing you everything no?
Google has already said that even the Webmaster Tools console will not show absolutely every link to your site. The best use of these tools is to monitor them for changes over time.
It still depends on google what links is quality to count as backlinks. It doesn't mean that if you build links with 500 links, all of your links would be counted in webmaster tools.