I think it is because they are different offences.
They aren't just being deducted points because they are crap, but because they have breached specific rules.
In this case is is being over 80 days late paying HMRC. Nothing else. They are actually 100 days late as it stands, so will likely be subject to a Winding up Petition by HMRC sometime in the future, when all this will be brought up again.
I suspect that the suspended points are likely to be applied once there is actually a buyer in place, otherwise the club is simply likely to go bust. I, for one, thing that they should just let that happen, but the EFL in its wisdom seem to want to keep Reading alive for as long as possible.
Given that the EFL is actually a members club, that isn't particularly surprising, but there does seem to be an inevitable demise that is going the way of Bury unless Dai actually does something positive.