Well, let's see.
1. Preprocessing data for entry. This might be used, for example, if you want to depreciate fixed assets using a method your accounting software does not support.
2. Post-processing data. You might do this if you have a report from an accounting system but your final report needs to take into account additional factors. Some of my customers use Excel to turn trial balance data from their accounting systems into financial statements.
Another example of post-processing might be if you take aggregated sales reports from an accounting system and further process it by business folk who don't know the programming environment.
As for paper: Yes, separation of duties is a part of it but paper has an advantage that no computer system can match, namely that if you keep your books in indelible ink, then alteration of numbers is obvious on audit. This is a weak point of electronic media. You can lock it down, but it is always possible for someone to unlock it. So with comparable policies, paper wins out anti-fraud-wise.