Don't need to apologize, wester - it's a useful question. The website leaves something important unanswered:
"But in some cases we must clear both your hand luggage and hold baggage at the transfer airport. The airline will tell you when this is necessary."
In my experience, airlines will tell you this - they also tell you this when it isn't true and not even necessary, like they just guess instead.
1. How does the airline checking you in know which cases require clearance at the transfer airport? The check-in might not be with the airline that takes you to manchester - so how does HMRC inform them (they may not even have a UK office) which rules to apply? Perhaps through an IATA or SITA working group? Any notes?
2. What are the cases where through-checking is not possible and HMRC 'must clear both hand luggage and hold baggage'?
I looked at the site as well - no leaflets or releases etc to airlines advising for through checking to UK internal destinations. (see if someone else finds out from the site in even less than 2 mins!)
Come to think of it, none of the posts have shown any 'official' guidance that the OP's bags can be through-checked through manchester to glasgow, and don't need to be customs-cleared at manchester first. The HMRC site doesn't confirm it, either.
Ron