Yes, ment the compiled format, the fileextensions sound too similar.

Basically for a clean approach, Assets and Descriptions
should be seperated.

Since the Textures are every time copied into the levelfile, it creates redundant data.
And thus blowing up filesizes.

Textures can also be reference by using somthing like
an "external" flag for a wad file.
Where the engine loads the texture then from the wad.
Just like it was done with the mdl format..
(Maybe even assigning textures as single files,
and not the closed WAD format)

And that palette file should be eliminated once and for all,
there is not purpose for it nowerdays.