Luggage check through and boarding pass are two completely separate matters.

Luggage will be checked through if the flight segment is part of the same ticket - so the passenger does not need to collect and recheck at transit airport.

If boarding pass is issued at origin airport, great. If not, it may be collected at the transit airport.

What happens if the passenger fails to board at the transit airport? Then the luggage won't be loaded for the onward flight; or if already loaded, it will be retrieved and offloaded. Irregular ops, messiness, tracking confusion, etc. happen - especially under stressed scenario when there are insufficient baggage handling resources at airports during this period of aggressive travel.