Got a chance to play around with this finally (on my new 40k pc no less. Got some thoughts/stuff to jot down as bug reports.
Addressing your points in a similar format.
My old machine used the same case.
Librarian Transfering bugged: Noted.
Librarian Powers: Fixed in the upcoming patch. They weren't using attacks, if by some miracle they did, the message was not displayed.
Forces on planet: You should be able to use 'Attack' instead of 'Raid', and make use of local forces that way. Otherwise you may have found more bugs.
Company titles: The plan is to let you rename them in 'Chapter Settings' and 'Company X', noted.
Chapter Log: Yep. I have to track down what alerts do not become part of the event log and change a line or two of code.
Apothecarion: Good idea. I believe there is plenty of room, although a portion of it will end up being saved for mutation tracking.
Wounded Lexicanum: No idea what happen with negative health marines surviving. Maybe it'll stay a feature?
Allocating Weapons: I'll take a look at this.
Planet Stat indicators: Yep.
WARP WINNING: This is fixed in the upcoming patch. If you end turn it should revert itself.
Odd Manuevering: One of the Ork ships seem to have ran for it.
Ship Selector: Under the fleet screen or loading/unloading marines?
Fleet Screen Troop Count: Running out of space near there, but it's possible I could add in a line saying something like Companies Present: I, II, III, etc.
Ship Capacity: No idea what might be causing that.
Purging: Noted. This will be fixed wtih the upcoming patch.
Purging II, Electric Booagloo: Yeah, Selective Purge, Purge with Fire, and Assassinate should be requiring at least a marine to perform. I'll fix this.
Equipment Portrait: Strange, I'll be taking a look at that.