The site:-query (site:sistrix.com) displays the number of indexed URLs that a domain has within Google’s index. The question of whether the order in which these results are shown has any importance, is a regular topic for discussion.
The last time we heard from Google about this topic was many 4 years ago, when Matt Cutts released a Google Webmaster Video. The core statements were:
We will sort the results through different factors. To do this, we use the estimated PageRank, but it is not exactly in PageRank-order
We also look at other factors. For example, the length of the URL.
The sorted list is a pretty good estimation of the interesting pages on a domain, though I would not consider it to be a perfect list.
John Mueller answered a question in the Google Product Forum on the topic. He wrote that he would not “really worry about” the order of the results, as long as the homepage for the domain continues to be indexed. You can check the index-status by using the info-query (info:https://www.sistrix.com/).
To find out how often we get the case that the homepage is not shown as the number 1 result for a site:-query. For this, we ran a site:-query for 10.000 domains and checked whether the homepage was returned at the top:
For about 95% of the domains checked, Google returned the homepage as the first result. Only around 5% of domains show a different result, where Google decided to show a sub-page. It is certainly easy for John Mueller to advise you to not worry about the order of results. If we assume, though, that there have not been any significant changes to the order of results, since Matt Cutts’ video, then your results for a site:-query should about mirror your own expectations of how important the pages on your domain are.