I'm sorry, I did not manage to follow what this "simpler" solution entails.
If you do not use the process "Uniform list of channels" anywhere, then the rows of EEG data (from the F matrix of the subject-level ERPs) that you want to average together are not aligned. In you grand average, the original subject-level ERPs would be averaged as if you had not changed the channel file.
If you don't call this process, you have to edit manually the subject-level ERPs to permute the channels left-right in the F matrices of the flipped subjects.
When averaging "data" files (EEG recordings), the channels are not matched by name. The matrices F in these files are averaged without any modification, regardless of the information contained in the channel file.