The reason this is a practical ISA is because quantum computers will be serve as co-processors to classical computers; hence the Fig. 1 illustration in that paper. The variational eigenvalue solver [0]; which is used to calculate the ground state of a molecule is a good example of the kinds of programs that this ISA will be used for. The QPU is only used to make calculations which can be sped up by a quantum computer; and the CPU is used for everything else.
[0]: https://arxiv.org/pdf/1304.3061.pdf