Label your layers and use a standard extension and tell your manufacturer to read them in and shut up. Or go to another manufacturer, its not rocket science its Gerber data and if your manufacturer cant do a simple little thing like this they are not worth using. They should work to your format and data, I have never liked the idea of using the extension to indicate the Gerber layer, its old fashioned and even when file names were only 11 chars long it was a pain, and only one or two systems outputted it that way. To use it in this day and age is dated.
I would tell the manufacturer to sort it as I have said, or you could just change the extensions yourself, but I don't agree with this process as it could lead to an error, so preferred get the manufacturer to sort your data, its then his responsibility and that's what you pay him for.