Great question regarding if pet rent is per pet or for all pets. The statute states that "[a] landlord shall not demand or receive additional rent from a tenant as a condition of permitting the tenant’s pet animal to reside at the residential premises with the tenant in an amount that exceeds thirty-five dollars per month or one and one-half percent per month of the tenant’s monthly rent, whichever amount is greater." C.R.S. § 38-12-106(2).
As you pointed out, the statute is unclear, and there is currently no case law interpreting that provision in the pet rent statue. A landlord's safest option would be to charge $35 for all pets. However, the statute states "tenant's pet," so there is a good argument the pet rent can be charged on a per-pet basis.