In Canada, the green levy excise tax applies at the manufacturers' level or at the time of importation. At the manufacturers' level, it applies when it is delivered to the purchaser, which is usually a dealer. So the underlying policy rationale for the green levy is not only to raise revenues but also to discourage the production of fuel-inefficient vehicles.
Presumably, the rental vehicle from, for example, the United States has already been manufactured outside Canada, so it would not be subject to the green levy. Then, when it's being imported for less than 30 days, it wouldn't be consumed in Canada, so the relief is applied on that basis. It would also probably be administratively more costly to administer at the border than to allow this relief for these very short temporary importations.