On site 1 , which has good link juice and authority the site: tool accurately reflects all the no's of site pages at root domain level.
On site 2 , with less link juice and authority the root domain site: tool command understates the no of pages. If the site: tool is used at a deeper folder level it reverts to the correct no. of pages in that folder.
So I'm wondering if there are issues in how the site tool is intended to work as site 1 is accurate and 2 is only accurate at folder level.