1) A stack-based ISA is still more space-compact. (AFAIR the Shi et al. paper mentions something like a 40+% increase in space requirement for the instructions.)
2) The performance improvement of a register-based ISA is only visible for interpreters that suffer most from instruction dispatch [1]. PHP is a rather complex programming language that is most certainly not bound by instruction dispatch at all. So I guess it could very well make sense to stick with a simple stack-based ISA, which incidentally is also easier to compile from the AST.
[1] for the sake of completeness: the stack architecture emits many instructions to push operands onto the operand stack. A register-based interpreter does not need those. Hence, the overall number of dispatches is lower, and if dispatch cost is your bottleneck the overall performance increases. OTOH, you need more space, because in addition to the opcodes, you need to specify/encode which registers to take operands from and put results to. (Hint: quadruple code and the likes.)