In almost all cases, you are more likely to lose quality with simple stereo instead of joint stereo because of the bitrate limit of MP3 - the maximum frame size is 320k. Sometimes, this is too little when using simple stereo because the encoder cannot exploit the similarities between left and right channel and has to encode everything twice. Using joint stereo is essentially lossless compared to simple stereo, it is just more efficient. All lossless codecs like FLAC or Wavpack also make use of joint stereo to improve their compression ratios.
BTW, you really shouldn't mess with the quality and VBR mode settings in CDex, just use Lame 3.90.3 or 3.96.1 as an external encoder with just the plain "--alt-preset standard" commandline. If you use the internal encoder in CDex, you should check which version it uses, it may be outdated.