As you have no existing structure to work around, I recommend the basement. Having that basement floor drain right there is always an advantage. HVAC systems must drain condensate (water that has condensed). If the system is in the attic, then this water must drain to the basement or ground level somehow. And as we all know, if a drain clogs upstairs and overflows, you will have damage.

Where is the ductwork? Obviously basement is the preference for the unit but putting in an attic is not that bad (if insulated). Sure there is the clogged drain but that will shut the unit down. Sure there could be a clog and a switch failure at the same time but that is highly unlikely since the system is designed so if the switch fails, it shuts down.

I have the same system in the basement except there is a pump. So while the attic system could leak and cause damage, the basement setup is actually more complicated (ie more things to break). And I don't know - flooded basement floor (carpet) might be just as bad as a wet spot on the ceiling. This isn't water under pressure kind of damage.

Thank you all - I will see if I can convince him to put both units in the basement. He was just mindful of duct reducing the ceiling height in the finished basement.

Are there any performance advantages of not having the unit in the attic? For example, ducts will not be exposed to unconditioned space but on the other side you need more ductwork to reach 2nd floor vs. ones on the attic and servicing 2nd floor. Thanks

The line set will be shorter. This improves the AC efficiency by a few percent.

Put the unit in the attic in an insulated space. The builder has the best idea.

Ducts outside of your living space is a big negative. When they leak, you blow your conditioned air outside. The make-up air comes from somewhere else, depressurizing your home somewhere else. Then you suck air in through random openings and cracks. In a humid environment this can lead to condensation and mold in some very interesting, sometimes hidden, areas.

In my neck of the woods, you would seal the attic and insulate the roof deck to put HVAC up there. You, however, are in a very different climate and I don't know if that is recommended there. If you ask your builder, they might not know because some of them are very conservative. If you want to educate yourself, try the Building Science Corp. web site. You might be a little late to do that. I would also suggest that you work with an experienced energy rater (Resnet).