Regiments and the army in total were not quite the rigid structure that we know of today. Most members of the regiment would be off doing things most of the time (e.g. bringing in crops, or just visiting home), when not on active campaign. (Even then the baggage train would often include dependents). Uniforms were not de rigeur, and arrived at haphazardly, as were procurement of basic necessities such as food, etc. Most officers were responsible for their own lodgings, equipment etc.
This lack of organization allows for a bit of corruption: Units indicating that they have more troops than they really do. Misplacement of equipment, supplies, etc. The rules already cover corruption of the Quarter Master General of the Army, with modifiers to the outcome, surely other levels of command can also be corrupt.
This change requires detailed finances worked out for each regiment, so the amount available is known. Then modifiers need to be made to results due to missing equipment, or penalties for discovery of corruption outlined.