If you can smell the sewer it must be (in most cases) open or opening somewhere in the basement area at the time your ejector pump drains the pit.
Some critical areas that can be responsible are:
Bathroom toilet around the base where the wax ring might not be providing sufficient seal
Basement floor drain if it has no trap, discharges into the pump’s tank below the waste water line (when the tank is full / before the pump is activated)
Poorly sealed sump pump tank / pit
Depending on the vent / sewer pipes material and their age, in case of cast iron and / or galvanized pipes, some might be corroded to the point where their walls have been breached and leaking sewer gasses.
PVC’s sometimes crack or separate at joints.
Siphoning shouldn’t happen unless there’s a clogged, missing or improperly designed / installed vent, or you have an “s” trap installed beneath one of the basement fixtures. If possible (and safe) you could check its roof termination for any issues (clogged with leaves, beehive, dead birds / rodents, etc.)
Switching the drain lines might resolve the sewer smell issue, however, in a properly designed and functioning plumbing system there shouldn’t be any sewer gas smell inside the house.
Please let me know how the investigation goes and if you have more questions.