Mixing itself is a pretty simple procedure, but people always forget about some key stages where sound quality can be an issue (i used to be one of those people). Dither, for one, since the audio application will be converting from its internal bit depth (probably 32bit) to 24 or 16bit.
It is entirely possible for an audio mixer application to have an impact on sound quality, just as a plugin or any DSP would have an impact on sound quality. How big of a difference is one of those questions that's difficult to answer.
Slackmaster 2000