What about redesignating NATO companies in those situations (ie, the x2 Marder, x1 M113 PzGren Bn) as "kampfgruppes"?
Seems I remember a FG85 campaign mod called Fulda Gap 81 (by Mark Breed?) which handled this dilema by modding the OOB as such:
" Company-sized Formations – Certain units of company size have an asterisk at the end of their name. These formations are coded as “Kampfgruppe” in the Order of Battle file. This was done so that they would not be penalized by the rules concerning fatigue and units designated as company or platoon. Many of these are specialized formations that normally operate as a company level formation and it did not seem appropriate to penalize them for their doctrinal employment (i.e. the ATGM battery of a motorized rifle regiment)."