Thanks everyone for the responses. I contacted the builder and relayed my concerns. They agreed that something is wrong. It looks like instead of placing the 3 front speakers on the front wall, they put them in the ceiling. They are contacting the audio people and will have them call me.
Yes, that is a good start but don't have them rush this. Best if you have floor speakers for the three fronts, hence the junction boxes low on the wall. Side and rear surrounds on wall would be better than in wall. Only the 4 Atmos in the ceiling. Also, make sure the subs are not by the front wall unless that is the only option.
There are better locations if possible.
Make sure they know what kind of speaker wire to use, at least 14 ga and perhaps 12 ga.. Interconnect cables with RCA connections to the subs.
From that ceiling screwup who knows what else is messed up.
HDMI to TV or projector from wherever the equipment is placed. If in a closet space, have good ventilation and you will need remote control sensors and wiring to it.
120V outlets at the sub locations.
Cat 6 cables for internet connection, streaming.
Now is the time to get it right, before framing. May want the cables in electric tubing so you can add, replace or whatever if needed later.And, perhaps, strings in each between outlet boxes so cables can be pulled in the future?
ps. ask them to label the cables at both ends which goes where so you don't have to troubleshoot which is which later.