Re: FMS VNAV and altimeter setting.
Can't speak for the Airbus, but Boeing VNAV usually gets its QNH from the Captains altimeter sub-scale setting. A cross-check is made to compare the sub-scale setting with that of the F/Os altimeter. Also the VNAV database knows the approximate transition level and flags a caution is still on STD.
Yes, if the setting is wrong (i.e. left STD set or wrong sub-scale) then the aircraft will not be at the correct alitude. Backup systems such as the rad alt, ATC radar monitoring and SOPs are designed to trap this error.
Also, there is a requirement to correct for temperature on certain approaches.