"Hidden" messages in Motorola messaging?
Partial answer (OP may update with findings later)


From my experience of Moto X Play messenger app - the count corresponds to unread messages.
OP is unable to identify unread messages. Proposed solution:


Use SMS backup &amp; restore to take the backup in xml format and open it on PC (browser, notepad or any other program) and compare with messages on phone to identify "hidden" messages. OP has been able to identify two so far
and  in the process of identifying other two.
Find out what is special about those SMS originators. Guessing, they could be contacts saved on SIM, or social media contacts or Google groups /Hangouts or contacts marked spam, blocked/ unknown contacts for calls, carrier messages or.... 
Once the nature of contacts is identified, take steps to treat them as other contacts whose messages are not hidden.