Wondering if the plumbing for the 5.5kw Heat Pump (for the Spa Zone) and the plumbing for the 8.8kw Heat Pump (for the Swim Zone) can come up through the base of the Vortex™ Hydrozone™ swim spa pool?

Yes, it can but you will need to make sure the trench, and cutout in the bottom of the swim spa base are large enough to accomplish this.