is this due to lack of confidence ( overall, not just b/c he is a freshman) or really wanting to redshirt him?
Not to answer for SFC but the staff doesn't think he's ready to run a college offense as of yet. He's still learning the playbook and they really don't want to waste a year of eligibility when he would have, more than likely, a negative impact.
Overall, you could argue that a move like this shows that they have more confidence in Thomas in the long-term. They genuinely feel like he is their QB of the future and no one would argue that 2021 Thomas is > 2017 Thomas. If they didn't have that much confidence in him then they probably wouldn't care about the lost year of eligibility. Just look at how many true Freshmen they have played, including a couple of guys who have only played on Special Teams so far (Smith and Mondesir).
Anything can happen between now and 2021 but that's the rational behind adding someone like this.