I suspect it was an oversight. When I fill out a report it asks for the check #, the amount of the bill and the amount of tip left. As long as my bill + tip does not exceed the maximum reimbursement and the tip was the % required, I will be reimbursed for the tip as well.
What does not work with them is to not have the tip written on either the bill or the credit card charge slip. To have the tip under the required % may jeopardize acceptance of the shop. To have the tip over the required % can lead to it not being fully reimbursed.
What they tend not to cover is valet parking which may be required where it is available.