The SDK shipped by id Software is a little "untidy".
You can download new versions of D3Game.sln, D3Game.vcproj, game-d3xp.vcproj and idlib.vcproj in this package.
They are in Visual C++ 2002 format but if you open them in a later version they will be automatically converted.
These files add the necessary changes to the projects to remove the warnings and to create output files in a folder at the same directory level as the source tree, rather than under it.
If your source is in 'C:\Mods\mymod\src' then the build folder structure will be this for a "Release" build...
C:\Mods\mymod\build\windows\release\game (gamex86.dll is here)
C:\Mods\mymod\build\windows\release\d3xp (gamex86.dll is here)
.. or this for a "Debug" build...
C:\Mods\mymod\build\windows\debug\game (gamex86.dll is here)
C:\Mods\mymod\build\windows\debug\d3xp (gamex86.dll is here)
The replacement package also contains a command script called PackPK4.cmd.
This script is run at the end of the build as a custom step. If you have 7-Zip (normal or command line version), WinRAR or WinZip (command line extension) installed then D3Game.pk4 will be created in the same folder as gamex86.dll for the current build configuration (Debug/Release).
If you want it to do so, PackPK4.cmd can also automatically copy the D3Game.pk4 file to the correct folder for it to run. Just edit the file and on line 9 replace...
set ModPakFile="C:\Program Files\Doom 3\mymod\mymod.pk4"
...or whatever folder and PK4 filename you want.