[red 928]

I suspect that the smell is from incomplete flushing, aka back-wash.
The system is not completely eliminating the urine and it builds up and smells.
Get rid of that complicated $80 flush mechanism.
It is not working well and will only cause
more problems.
Convert the toilet back to a conventional flapper-style.
it's easy to do and should cost less than $30
but you will have to remove the tank to do it.

EDIT I just re-read the OP and the above diagnosis would not
explain the lower static water level.
That lower level could only be caused by a crack in the toilet
allowing water to drain to the current level (unlikely, never seen that before)
or caused by excessive syphoning.
That could be why the above comments about venting are relevant.

I would still get rid of that POS water saving flush system