I think Ellen Ryder may have some explaining to do...

It just spoils the plot twist that both twins were adopted. In reality they are underwear models implanted with fake memories, sent to space to become mindless killing machines and take over all the other galaxies. Alec was just a front for the organization transporting them. Ellen never even existed.

In less serious terms, it's because the number of headset the dad uses is tied to the headset Ryder used and is pretty usually some iteration of the male headset of the same number. So you used headset 9, so dad becomes an altered version of Scott's headset 9 head. Which in this case makes the family connection look quite odd.
Or maybe Alec underwent a questionable facial surgery and now his supermodel genes are appearing in his children. 

Well they do try to make them match. Problem is that some of the heads have more limited skintone range than others. So 0.10, which is usually pretty pale on some of the headsets looks tan on others. Not sure if lazy is the word I'd use, but it is very awkward.

Jase Dakota Alec follows the face of the Ryder you are currently playing. So if you want the dad to have the same face as in the first run, you'll need to use preset 6 (I think) for Sara.