He inherited a good team that never won. I don't think the sample is too small at this point, even if it's premature to say that he is the best Phillies manager of all-time just because he's already has the highest WP of all-time (behind only two partial-season guys in 1890). He's a good manager. Another one would not be better. And probably half of them would still bat Schwarber lead-off.
And yeah, Schwarber is not getting on base a his usual pace so far, but he was third on the team in OBP last year (behind Marsh who was not a full-time player, and Harper who is never going to lead-off) and has been a good OBP player and leadoff hitter his whole career. I disagree (strongly) with the idea that a manager should make decisions based on just a month or six weeks.
And clearly one of Thomson's strengths as a manager is sticking with what works and making his players feel comfortable with roles and routines. There's no sabermetric for that, admittedly, but tinkering with the line-up might add one win in tactical advantage while costing them one win in chemistry disruption.
They tried Turner leading off last year and it was a bust, though that was mostly because Turner was a bust (at the time). Stott was also a leadoff bust, since he was (and still is) a work in progress.