In Metal/Rough, there's just 1 texture for color information (the base color/albedo), and the metalness map (the roughness map) determines in effect, how the lighting will behave. In Spec/Glossy there's two, one for diffuse lighting (stuff that isn't shiny) and one for specular lighting (stuff that is shiny). If you look at your -reflect map, you'll see how its very similar to your base color map.
Look at the image below and you can see how the maps differ between the two workflows. The base color map has the colors you expect, but the diffuse map has none of the shiny blue color info, and likewise, the specular map has none of the dull dirt color info.
So on our typically shiny spaceships, the diffuse map may seem
darker, but both diffuse and specular would be working together to make it look right.
When you put the textures in game, do you find the ship is noticably darker? Do you have any side by side pictures from your older exports to using my presets?EDIT: Actually no matter what you'll probably find it brighter because no matter what, diffuse is going to be different from your original exports. If you're comparing images from SP to FreeSpace, don't do it in the F3 lab since F3 lighting is apparently different than a normal mission.(Note I'm not a graphics wizard, but I did read a web article or two)