2 Questions Concerning .tga and .dds Files

what do I do about the ada_dress.tga? Do I still have to map it to a .dds file, or should I leave it unmapped lest it result in two body models clipping with each other in the game?

VERY CONFUSING. but I will try my best to help. What you shoudl do is select all layers in Milkshape3D and press HIDE. The one by one unide the layers to see which ones are needed. If there are undeed layers simply remove them and remove their assigned textures so long as they are not being used by other layers

should I leave it unmapped lest it result in two body models clipping with each other in the game?
im not sure what you mean here. Are there conflicting meshes? If not then dont worry, just remove the texture that isnt being used from the materials list. 

First things first though.. .
I suggest you read Son of Persia's tutorial on converting 2007 mods HERE .Its a good idea to get info from the guy who invented the tools

Ok as for problems with the Maroks tutorial I can not speak to that. He does things a bit differently than I do when it comes to textures. When it comes to starting a mod I do this:

-change the skeleton Son of Persia's Skeleton Changer Tool
-import the changed.smd into 3d program. 
- convert all diffuse textures to .dds format (DTX.5). Leave transperant textures to be used as .tga or dd.s doesn't matter. 
-rename all textures I am going to use to their names as would be seen in the pack file. example:

Ada_body.tga---->0024.dds
ada_ribon.tga---->0025.dds
ada_holster.tga-->0026.dds

- import these newly named files into the 3d project
- apply these textures to their meshes
- clean up mesh, and/or fix bone assignments if needed
- export as SMD to name of characrter im replacing. example: export to pl16.smd
- export OBJ file to create an MTL file that the BIN tools need
- edit MTL file to have all textures in the materials to be in sequential order. Example:


#
# pl16_001.mtl
#

newmtl 0065.dds

illum 2

Kd 0.800000 0.800000 0.800000
Ka 0.200000 0.200000 0.200000
Ks 0.000000 0.000000 0.000000
Ke 0.000000 0.000000 0.000000
Ns 0.000000
map_Kd 0065.dds

newmtl 0066.dds
illum 2
Kd 0.800000 0.800000 0.800000
Ka 0.200000 0.200000 0.200000
Ks 0.000000 0.000000 0.000000
Ke 0.000000 0.000000 0.000000
Ns 0.000000
map_Kd 0066.dds
map_D 0067.tga

newmtl 0068.dds
illum 2
Kd 0.800000 0.800000 0.800000
Ka 0.200000 0.200000 0.200000
Ks 0.000000 0.000000 0.000000
Ke 0.000000 0.000000 0.000000
Ns 0.000000
map_Kd 0068.dds

newmtl 0069.dds
illum 2
Kd 0.800000 0.800000 0.800000
Ka 0.200000 0.200000 0.200000
Ks 0.000000 0.000000 0.000000
Ke 0.000000 0.000000 0.000000
Ns 0.000000
map_Kd 0069.dds

- save MTL file after editing order
- edit the 
Bin generator.bat file to point to the correct texture pack file and texture index in the TPL. Example:
RE4_UHD_BIN_Generator.exe pl16_001.smd pl16_001.mtl 01000016 65 
(in this example the value 65 would be changed to the number of your first custom texture as it appears in the pack file)

- check the newly generated TCS file to ensure that all textures read properly/ Example of proper texture mapping:

file 65= 0065.dds
file 66= 0066.dds
file 67 = 0067.tga
file 68 = 0068.dds
file 69 = 0069.dds

- rename newly generated TPL from pl16_001.tpl to pl16_002.tpl (or whatever the TPL is in the original udas folder)
- replace original pl16_001.BIN & pl16_002.TPL with newly generated ones. 
- repack pl16.udas
- rename pl16.udas.lfs to pl16.udas.fls.bak
- copy new pl16.udas to BIO4\Em\ folder. 

"Some of the .tga files that I converted into .dds files (in both the 2007 mod and the Ada model from the 2007 version of the game) do not appear in the textures list for pl16a_changed.smd (see above) when I open it in Milkshape 3D. One such .tga that appears in both the 2007 mod and the Ada model from the 2007 port is ada_te.tga (see above) so I had no .tga to map a .dds tool".

First let me say that if the game reads a model that had an MTL with:

file 65= 0065.dds
file 66= 0066.dds
file 67 = 0067.tga
file 68 = 0068.dds
file 69 = 0069.dds

and all the files in the pack file are:

file 65= 0065.tga
file 66= 0066.tga
file 67 = 0067.tga
file 68 = 0068.tga
file 69 = 0069.tga

it doesnt matter. The game reads them as the same. SOmetimes there are parts of models that dont get used when we convert them and there are extra textures left over. If this is the case you can simply leave them out, so long as your model looks ok and that the model is not calling on textures that arent there.