if you haven't done either of thomas' chapters before completing all of the main character's third chapters, the game will give you a prompt asking if you are sure you don't want to complete thomas' chapters before moving on to chapter 4, as they will become locked if you select to move on to chapter 4.
personally, I prefer to play through chris's and hugo's chapters as such:
geddoe and thomas i tend to do all at once (geddoe 1, then 2, then 3, thomas 1 and then 2), and i don't have a preference for playing their chapters before, after, or in the middle of chris and hugo's plots. whilst chris and hugo are fairly intertwined, geddoe and thomas are much more isolated stories. one thing nobody has pointed out is that you get to see a couple of extra scenes in thomas's chapters if you play them after unlocking thomas in all three main POV(basically it's the thomas perspective of meeting geddoe and chris).
another interesting point is that if you decide to do the chris level 99 trick, it might make more sense to play her chapters all together, and early, just so you don't accidentally recruit those stars with main-char-level-dependent starting levels. of course, if you're are doing that, you probably have already played through the game once, and so you can afford to miss scenes you've already seen.