That made a lot of sense, thanks so much for your reply!
Unfortunately this doesn't seem to work for stock command pods I was able to access the UV maps for the stock command pods, but they don't seem to have a separate model for the windows. Here's what I found for the Mk 1-3 pod:
-------------------------------------------
Mesh Name Model: M1-3
Render Type: MeshRenderer
++++++++++++++++++
Material #: 0
Material Name: M1-3 Pod (Instance)
Shader Name : SSTU/PBR/Metallic
RenderQueue : 2000
_MainTex : Squad/Parts/Command/Mk1-3Pod/M1-3 Pod (UnityEngine.Texture2D)
_MainTexOffset : (0.0, 0.0)
_BumpMap : TUTextureColor:0.5019608:0.5019608:0.5019608:0.5019608 (UnityEngine.Texture2D)
_BumpMapOffset : (0.0, 0.0)
_MetallicGlossMap : TUTextureColor:1:1:1:1 (UnityEngine.Texture2D)
_MetallicGlossMapOffset : (0.0, 0.0)
_Emissive : Squad/Parts/Command/Mk1-3Pod/M1-3 Pod_GLOW (UnityEngine.Texture2D)
_EmissiveOffset : (0.0, 0.0)
_AOMap :
_AOMapOffset : (0.0, 0.0)
_Smoothness : 0.7
_Metal : 0.25
_Color : (0.8, 0.8, 0.8, 1.0)
_EmissiveColor : (0.0, 0.0, 0.0, 1.0)
_MaskColor1 : (0.9, 0.9, 0.9, 0.0)
_MaskColor2 : (0.9, 0.9, 0.9, 0.0)
_MaskColor3 : (0.9, 0.9, 0.9, 0.0)
_MaskMetallic : (0.0, 0.0, 0.0, 0.0)
++++++++++++++++++
-------------------------------------------
-------------------------------------------
Mesh Name Model: Flag
Render Type: MeshRenderer
++++++++++++++++++
Material #: 0
Material Name: rocketScience
Shader Name : KSP/Alpha/Cutoff
RenderQueue : 2450
_MainTex : Squad/Parts/Command/Mk1-3Pod/M1-3 Pod_GLOW (UnityEngine.Texture2D)
_MainTexOffset : (0.0, 0.0)
_Color : (1.0, 1.0, 1.0, 1.0)
++++++++++++++++++
-------------------------------------------
I did see that "emissive" texture, which appears to be the one used for glowing windows (this is consistent for all parts with windows). Unfortunately, copying "excludeMesh = M1-3 Pod_GLOW" into the config file didn't work. Not sure what else to try...