Monkenstick
There are three possibilities in our scenario:
1. The retroviral sequences were originally designed in and had an initial (pre-fall for example) beneficial role.
2. The retroviral sequences inserted during the fall.
3. The retroviral seqeunces inserted deterministically at some other time via DNA motifs and hence incorporate relative to phylogenetics.
It is good evidence of common descent, don't get me wrong, but it has possible answers in our scenario.