Placing the MPS 400 flow sensor on the bottom of your case should not induce any issues. If I understand the device correctly, the flow rate is determines by reading the pressure differential on either side of the orifice in the internal flow path. There are no moving parts, other than the coolant, so vibration is not an issue at the flow rates anticipated.
The only issue to consider is no angular fittings at, or with 5 cm, of the inlet/outlet ports, as they may cause turbulence in the coolant stream at the orifice, which may give erroneous results.
As to the temperature port, I do not know if temp data is passed over the aquabus to the aquaero.
If it is, you can use the MPS flow temp port for the aquaero... I have never tested that.