What technique is most likely been used in achieving such obfuscation ?
PHT means “program header table” and is one of the two tables describing the layout of the ELF file. The PHT is the one used by the OS to decide which parts of the file are mapped at what addresses in the memory.
The ELF specification does not specify what should happen if the segments in the PHT overlap, so the actual behavior depends on how the loader is implemented. If the OS behaves differently from IDA, you may see an incomplete picture, so it may be best to run it in debugger and see what actually ends up in the memory.