Actually it makes a sort of sense, as the Land Raider Proteus was primarily an hazardous exploration vehicle, not a front line combat machine like the Mk2B.
It's not Heresy, as long as the Emperor signed off on it.
Remember that Inquisitors and Rogue Traders get an 'out' in terms of Imperial Restrictions because they are considered to have Imperial Authority - i.e. they speak directly for the Emperor in their sphere of authority and can grant themselves an exemption in a way a Guard officer can't.
True, but in the case of Land Raiders you have a direct instruction from the Emperor that they are to be used only by the SMs. Even someone who claims to 'speak directly for the Emperor' may have trouble directly flouting his instructions. While an Inquisitor or a RT might be able to get away with using them, it could be problematic (it would essentially come down to who has the most influence - the RT or the person accusing him of Heresy).
Amusingly the Emperor's instruction re: Land Raiders was just an emergency measure due to the Horus Heresy. Until then LRs were split between the marines and the Imperial army, but due to the war there was a shortage. The marines needed as many as they could get hold of, so the Emperor essentially just ordered all loyalist forces to turn over their raiders to any marines that wanted them. It was only meant to be a temporary measure... but then it became holy scripture.