Well, regardless of what the GOM says, all FOs come in with less than 1200 hours, fly in the right seat as an SIC and then get to upgrade to PIC when they hit 1200 hours. Being that the 1200 hour total time is in fact an FAA time requirement to act PIC under Part 135 flight rules, the company could not legally allow that pilot to upgrade if they couldn't log the time.
Also, many SICs wont even accept an upgrade to PIC in order to not be locked into another contract so they can go off to an airline when they hit ATP minimums, so airlines accept the logged time.
All this to say, argue all you want about it, everybody is logging the time and it is being accepted not only by the company, but even by large regional airline companies.
If you are a BTQ copilot, LOG IT!