One of the reasons why BSP Factory does not import the lightmaps is because it supports both Half-Life and Quake BSPs. Quake BSPs have very low quality lightmaps (grayscale lightmaps!), and even Half-Life lightmap quality is slower than the ones than BSP Factory generates.
With BSP Factory, you can import a Quake1 BSP and generate full-color lightmaps in BSP Factory. I don't know if you can do that in Unwrap3D. I'm sure that Unwrap3D is a great tool, but it is impossible to make an application that fit the needs of every programmer. I'm sure that there are a lot of happy Unwrap3D customers. I'm sure there will be some people too that will find more suitable to pay 15$ for BSP Factory.
With BSP Factory, you can import a Quake1 BSP and generate full-color lightmaps in BSP Factory. I don't know if you can do that in Unwrap3D. I'm sure that Unwrap3D is a great tool, but it is impossible to make an application that fit the needs of every programmer. I'm sure that there are a lot of happy Unwrap3D customers. I'm sure there will be some people too that will find more suitable to pay 15$ for BSP Factory.