Have a flight coming up with INTL -> CGK (21 hour layover) -> DOM.

Checked in online for INTL -> CGK, but was instructed to pick up boarding pass at airport -> I presume this is for document check.
However, the check in site shows that I cannot check in for CGK-> DOM and must check in online. Does this have to do with the layover ? Can I check in at airport with the first sector or can I only check in, in person, at counter at CGK once I arrive at CGK ? Any insights as to why ?

Of course I only want my bags tagged to CGK to begin with as I have to overnight there and would only drop my bags off the next day anyway.

The return sector DOM -> CGK (3 hour layover) -> INTL shows that online check in would open 48 hours before my departing flight.