Because Fluid Grid Layouts put media queries into the Fluid Grid CSS file.
Media Query Manager puts media queries into the <head> tag of your HTML doc with links to separate external style sheets for each device. They're just way too different things that don't work well together.
DW associates the FG pages to Fluid CSS, which it asks you to create/attach, while creating a new Fluid page.
By doing this is gets the location to update when user makes any changes to existing element or adds a new element.
There is no dynamic way to change the pointer to custom media queries on the fly.
Please feel free to raise a feature request @ https://www.adobe.com/cfusion/mmform/index.cfm?name=wishform, mentioning the same.