As you say, the very fact that we know the real direction counters that. They mean that within the abstract context of electronics presented in introductory physics, the real direction of charge doesn't matter and cannot be determined. As long as you pick one consistent convention and stick to it, the math will always work out the same, since depending on convention, all the directions and signs are equally flipped. The real direction of charge only matters when you get deep into the details (eg semiconductors).

At the level of detail of introductory physics, it's effectively a symmetry, similar to how given the simultaneous flipping of charge, parity and time, you cannot tell the difference.