It still doesn't explain why the statues of the two lost primarch were removed from that garden in the Imperial Palace. Even years into the Heresy the traitors' statues were only covered in cloth. That might lead you to believe that they did something far worse than merely attempt to overthrow the Emperor of Mankind.
Would losing your legion to an obviously hugely powerful enemy be that something? I don't think so.
Losing two legions and their primarchs may have been tragic enough in the context of that time period to justify their statues being removed. At that point it was probably inconceivable that primarchs would ever turn traitor, but having primarchs die was a tragedy worthy of note. Worthy of the symbolic removal of their statues from among the ranks of their brothers.
The other statues simply being covered isn't necessarily an indication that the circumstances were somehow less significant. The Emperor himself is credited with expunging the two missing from records, it is possible it happened at a time when such a thing could still be hidden from the greater Imperium, while the later transgressions during the Horus Heresy could not be so easily buried.