I agree; however the best practices work around is as follows:
Put pet fee in your rules, with statement that it is not included automatically and will be charged after guest books but before check in.
After reservation is made, click "report a problem" --this sends you to resolution center.
Ask that guest for the pet fee; click "additional services" and explain it is for the pet.
Guest must pay before check in.
Note mosts hosts handle their taxes in the same way (that AirBNB doesn't collect). There is no deduction for the "extra services," so that helps with your tax accounting.