It's not so much an issue of it being above 90%, as it is an issue of charging more than 90%; especially when you are dealing with batteries which contain multitudes of cells. The two main factors are: 1) You aren't monitoring each cell separately, so you may be overcharging a few cells which have already hit 100% while the other cells are still below 100%. 2) It puts more stress on the cell when packing that last 10-20% into the cell. Once the energy is stored, it doesn't put any more stress on the cell sitting idle.
And as a point of clarification, the rule of thumb is generally considered to be 80% for Lithium-ion. This tends to create quite the debate. Tesla lists 90% for their distinction between daily and trip, which there are a ton of speculation / assumptions as to why, but as for the basic Lithium-ion cell chemistry goes, the rule of thumb is 80%.