Matron is the person who Squall / Co. remember fondly. A person who was kind, nice, lovely and helpful back then. These things are what the party fond of and therefore they simply call her Matron. Squall even calls Edea Matron later in the game, which proves that Squall rather calls her Matron instead of Edea. So, why should they call her Edea, instead of Matron?
"Nannie is the person who Kermit / Co. remember fondly. A person who was kind, nice, lovely and helpful back then. These things are what the muppets are fond of and therefore they simply call her Nannie. Kermit even calls her Nannie later in life, which proves that Kermit remembers her as Nannie and not anything else. So, why should they call her something other than Nannie?"
Your argument, in a nutshell.
They were kids growing up calling her by her title 'Matron', so it became ingrained. Edea is her name. Matron is her title. She would be Matron Edea Kramer.