Inerting a wave soldering machine will improve the wetting of both pads and components, reduce the demands made on the flux, and almost eliminate the build-up of dross. On that basis you would expect any problems due to poor solderability or joint quality to disappear. However, using an inerted wave soldering machine might just create problems with solder balling, should the solder masks chosen be incompatible.
Improved wetting will probably reduce the overall level of touch-up needed, as spikes, shorts and other signs of poor drainage will be considerably reduced. Drainage will be particularly enhanced by using the selected de-bridging capability in areas (such as connectors) where there is a high concentration of wave-soldered joints. The overall improvement in solderability may also give the designer the freedom to use less aggressive fluxes, perhaps changing to a no-clean or low-residue type, or to use an alternative board finish, for example an OSP to replace HASL.