Welcome to another Wing Commander edit. This scene never really worked for me in the theatrical cut. It feels like it's missing something, and while I'm no pro editor I do feel like it's missing a bit of connection. They tried to play up him being awkward and I'm not sure they ever quite get to him sounding sincere. More than that, this scene really should be motivating Blair to actually figure out what Pilgrims (and therefore his heritage) is all about. I haven't changed the scene drastically from the theatrical cut, but it has two minor additions. I've taken the opportunity to have a little fun with the edit and incorporate some alternate takes of some parts that help give the scene a different feel.
For the changes, I feel that Maniac directly referencing the Pilgrim's place in history is relevant. I think it's a nice addition. The problem with the way the movie is shot though is that some of the best takes in my opinion are only shot in the wider angle, so it does mess a bit with the style of the original editor who - typically - prefers a rhythm where the scene starts wide, goes to a mid shot and then is told almost exclusively in alternating closeups from then on. Still, I feel the scene works well enough here.
The other addition is the coda. This scene normally should be followed directly with the scene in Paladin's quarters. The scenes got juggled around in the final edit, but here I feel having Blair look at his cross and get out of bed helps sell the flow thematically between this scene and the next. As a side note, the shooting script has a small interchange with Merlin after Maniac leaves where Blair first asks Merlin for info on the Pilgrims. That helps spur Blair to go see Paladin. However, they do not seem to have bothered filming that merlin bit, and ultimately with Blair looking at his cross that interchange really isn't necessary
I think a lot of the way movies are made has evolved a lot since 1998. Everything is digital now so it's easier to review and update your footage. Productions make lots of notes regarding the DP and Director's choices for favorite takes and other elements like continuity issues, but going back to change footage you had previously settled on was probably more of a chore once you had already built a whole scene around a specific idea or set of complimentary takes. The final choices are often not necessarily wrong but are made to support changes or deletions of material.
