There is no concept of Indirect or Beneficial Ownership in Indonesia. Indonesia will only look at the direct ownership in determining tax. Foreign trusts would be treated as a separate legal entity for local tax purposes.
With this said, Indonesia does have a separate law dealing with foundations, or what are commonly called Yayasans. Recent changes in legislation require these to be for certain charitable, educational, religious or other not-for-profit purposes, in which case they can be considered as tax exempt entities.