No it won't affect the bake, just pointed it out in case that'd be something noticeable in the game you want to put this in (it probably will be). Generally to make characters pose, you want to use a skeleton rig so that you can move the bones around to make the pose you want. I'm attaching the blender file here, feel free to use it (or anyone else reading this). It was made for a character ported from another game but it should work fine for the Sith trooper model with a few adjustments. This way, your models won't need to have holes everywhere.
I use Blender 2.8+ which I definitely recommend, unless you really need 2.79 for some reason (such as plugins that don't exist for 2.8). The general process goes like this:
In Object Data Properties, under UV Maps, create a new UV map. Name it however you want. Do this for each of the meshes and make sure they all have the same name name for that second UV set.
For each of these objects, click on their new UV set and proceed to unwrap your model however you want. There a different possible approaches here. You can make sure you don't hit Unwrap and just rearrange the UVs as they exist in the first, original UV map so that all of them fit into one image. Or you can select everything, hit U, 'Smart Unwrap' and call it a day.
Once your second UV set is ready, duplicate your objects. Rename the duplicates into something like "[NAME].orig". Name the others something like "[NAME].new" (this is just to make these instructions clearer). On the .orig meshes, delete the second UV map you've created. On the other meshes, delete the first UV map so as to only retain the UV unwrap you've created.
Now for each mesh: Select a .orig mesh. In the material node editor, add an Image Texture node. Create a new image and name it "MyTexture" or whatever, with the resolution you'd like. Whether no alpha channel is need depends on your target game engine and the results you want to achieve. Make sure the new image texture node is active. Now, CTRL + select the corresponding .new mesh. Create a new material, set it up as a simple Image Texture -> Diffuse BSDF -> Material Output, with the "MyTexture" image selected in the Image Texture node. Make sure the Image Texture node is selected here as well. Now go to the render tab and select Cycles. Scroll down to Bake and select "Diffuse" in Bake Type. Uncheck "Direct" and "Indirect" under Influence as to only retain "Color". Click on the "Selected to Active" checkbox. Hit the "Bake" button, and after a few moments your MyTexture image should contain the texture information of the mesh you've baked. Repeat the process for the other two meshes, just make sure that "Clear Image" is unchecked under Output or Blender will just keep erasing whatever you had baked before.
There's probably a shorter way to do it but this works every time.
Unfortunately I can't help for the Unity part. AFAIK, Blender Render is longer worked on and has been replaced with Eevee in 2.8+, but you'll want to use Cycles to bake your new texture.
basic armature.fbx