IIRC, there is no non-RP reason to duplicate HQ elements to lower chance of beheading strike in current (1.9.5) version, because there will be no battle-replacement commander, and any other element will play the same role of diverting enemy fire from your HQ, and battle elemets will do it better, and they will do damage at the same time, in contrast to spare HQ. In other words, probabilities of any commander death from enemy fire, drop fail or accident are all independent from numbers of HQ elements in their formations. The only case where you can use spare HQ effectively during local combat - is the case, when you have a destroyed HQ, have a spare HQ in the same formation, and have no RP rule to not appoint another commander of the proper rank just during the same local combat. That will be little cheating, though.
And I'd prefer to have some logistical elements in my drop-companies - they go out of ammo quite promptly, fighting with usual battalion-size garrisons, and henceforth cannot use their better training effectively.
As for specialized boarding troops - I haven't tested it yet, but I think they have to be lighter: improved weapons make them larger by quarter (so less elements in the company), while their increased armour-piersing being most likely useless against very lightly armoured enemy crews.