We have been leaving the symbol pins blank and naming them in the Part editor. That way we have generic symbols in the library which can be configured differently in the part editor. The more I look at this method the more I think it would be better to name the symbol pins and make the necessary adjustments in the Part Editor. I wonder if slotting and pins swapping has something to do with this.
Thanks for your comments,
It is a question of scale. For instance smaller slotted parts with different pin outs for different packages are better numbered in the PDB - that way you have fewer symbols. But larger parts or those with only a single cell it is better to number the symbol and import the mapping into the PDB. Where you make the distinction is down to personal preference.