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If we say there are two 512x512 textures, you should just use a simple image editor to put them beside each other in a new 1024x512 image, and use that as a texture. Then you should select the part(s) of the mesh that use(s) texture A, and scale its(/their) UV coordinates to be 50% the previous size, on the X axis, and then move them to the left half of the texture. Then do the same for the part(s) of the mesh that use(s) texture B, but moving those UV coordinates to the right half of the texture instead of the left one.
Firstly, compiling for what? Secondly, I explained that in my previous comment, though only for 2 textures, but you can easily just do what I explained further than what I explained, with tiling more textures beside each other and scaling the UV coordinates to lower half multiples and moving them appropriately.
If you have texture A and texture B, then look at the UV coordinates for both, you will find that they will likely cross over each other. Even though Blender will show both textures' UV coordinates simultaneously, they won't necessarily belong to the same texture, meaning that though they appear to cross over each other, they may very well be entirely separate from each other due to using different textures from each other. The same goes for 20+ textures, of course. And there's not really anything that appears to be that "wrong" about how the "before unwrap" thing looks in the 3D viewport in the screenshot you posted.
Does the model use multiple different materials in Blender? If so, it should already be set up correctly, you just have to assign each VMT material in Source the correct texture(s).
If not, does the model use multiple different objects in Blender, one for each texture? If so, assign a different material to each object.
If not, does the model use multiple different textures in Blender already? If so, select each face belonging to a specific texture, then make a material for that texture and assign those faces to it, and do this for each texture.
I repeat: There is no reason to want to combine the textures into a single texture for Source engine models.
When you compile a model for Source, it will look for a VMT file (material) for a material of the model. If the DMX/SMD model has a material called "body", that's what the Source engine will look for when trying to load the Source model in question.
How much experience do you have with making models for the Source engine?