The only difference between the one-step/two-step arrangement is timing and convenience, it has nothing to do with the quality of the resulting files

Unless of course doing the two in one go causes the ripper to make bad quality rips, which you have to be careful with on low end machines.

For example when I used to use AudioCatalyst if I selected the option to encode on the fly as it was ripping it often caused the rips to end up bad (even through no ripping problems were reported).