That's how it works in Mount & Blade sadly. Bodies and heads are actually separate items, kinda like being a helmet and armor that you can never unequip. If you change any torso color it'll change all the torso colors for all characters. It's one of the secrets to Mount & Blade's ability to have 1000 troops on the field, though, so it's hard to complain about it. It isn't about making an attractive character so much as it is about being on the field with hundreds of other ugly dudes and stuff.
Instead of that, we can try to mod it so that nobody is naked in training. I never understood why we had to be naked in training anyway. Yeah they'll say it's about having 0 armor rating and weight for no encumbrance and stuff, but why not just give everybody some special training armor with 0 armor rating and 0 weight? Some other mods have already done that, and it isn't very hard, but nobody's done such a submod for Floris yet.
Anyway, about the "vanilla" heads... It's all kinds of tedious things to do to remove the graphical updates Floris added.
My personal advice is just get used to it. However, if you really want to put yourself through it and you're okay with tinkering game files, I'll point you in the right direction. As early as now I'll wish you good luck and I hope you're up for it because it's gonna be a repetitive and tedious process.
0. I recommend you take a look at
this thread. It isn't really important for what we're trying to do but it'll give you an idea for what needs to be done.
1. Just like in that thread, download and install
OpenBRF. Read its documentation if needed, though I will give you some tips on what to do anyway.
2. Back up and open the file <your warband directory>/Modules/Floris Expanded Mod Pack 2.54/Resource/min_fac_materials.brf. If you installed OpenBRF properly it should open simply by double-clicking. This is the face textures file and we'll be editing this stuff. You should probably only edit one or two of the faces as needed. Preferably only the one you're going to use. The reason for this is that there are more face types in Floris than there are in Native.
3. Let's use fac_manface_black01 as an example, since I assume it's one of the faces you're interested in changing due to your comments. Click on fac_manface_black01 on the left panel and you should see a creepy-looking face with a weird expression spread out on the right panel. In the middle panel, we'll be editing the values there to match the ones used by Native.
4. Open up <your warband directory>/CommonRes/materials_face_gen.brf. This should open up in another window. You'll see some more creepy faces in there.
5. Click on manface_african.
6. Copy all of the values in the Data panel in the middle from materials_face_gen.brf to min_fac_materials.brf.
Shader: Don't touch. Already the same as Native (faceshader_high_specular).
DiffuseA: manface_african
DiffuseB: manface_african_old
Bump: man_normalmap
Enviro: Don't touch. Already the same as Native (none).
Specular: Don't touch. Already the same as Native (man_old_normalmap).
Copy also the Spec RGB and Coeff values.
As you do each of that you'll notice the textures change and look just like the one in Native. That means you're doing it right.
7. Do the same thing for Shader, DiffuseA and DiffuseB for the fac_manface_black01.LOD. Don't add a bump or specular map to this. Make sure Spec RGB is 0.000 for all values and Coeff is 1.000.
8. Save. Test in game.
You probably already have an idea of how it works by now. As for the hair textures, they're also located in those folders. Look at min_fac_hair, etc. You can probably figure out how to do it from there.