It can be done, but you don 't save file size by doing it.

The total size of the download will not change whether the files are inside the .BSP of as separate files, the only difference is going to be that when embedded there will be no clutter of files in people's folders and people newer to handling custom maps will find the map easier to add to their map collection/server since there is only one file to place in a very easy to find place.

The Source engine doesn't use WAD files, the closest you can get to what you want is a .res file which is basically a txt file listing textures and the location of the textures for the download. It just doesn't make sense to use res files anymore since zipping the files into the bsp is just so much easier and eliminates a lot of the problems for inexperienced server operators.

Did you maintain the same folder tree in the bsp with pakrat?