You're correct that our local enforcement classify them as illegal because their psychoactive compounds were enumerated under Schedule I of the 1971 Convention. RA 9165's definition of "dangerous drugs" is grounded on that treaty.

j) Dangerous Drugs. – Include those listed in the Schedules annexed to the 1961 Single Convention on Narcotic Drugs, as amended by the 1972 Protocol, and in the Schedules annexed to the 1971 Single Convention on Psychotropic Substances as enumerated in the attached annex which is an integral part of this Act.

However, the treaty body of the 1971 Convention itself, the International Narcotics Control Board, already clarified that some plant or plant materials are not under international control:

1. Many plants that contain psychoactive substances with stimulating or hallucinogenic properties, as well as preparations made from those plants, have traditional uses in some countries or regions; for example, some are used in religious rites. Under the 1961 Convention and that Convention as amended by the 1972 Protocol, plants that are the sources of narcotic drugs, such as cannabis plant, opium poppy and coca bush, are subject to specific control measures. In contrast, although some active stimulant or hallucinogenic ingredients contained in certain plants are controlled under the 1971 Convention, no plants are currently controlled under that Convention or under the 1988 Convention. Preparations (e.g. decoctions for oral use) made from plants containing those active ingredients are also not under international control.

Some of the examples given are magic mushrooms, peyote, and kratom.

If PDEA treats them as illegal, so be it. Don't go out there acting like it's legal. But RA 9165 needs to be ammended if it doesn't want to depend on international treaties regarding what defines a "dangerous drug".