No, don't trim them until after the daggerboard trunk is installed (unless the plans and directions say otherwise). The ledger posts normally extend past the bedlogs and through the bottom panel, and are later trimmed off flush with the outside bottom of the boat.

Old Yeller

There are some words about this in the skerry manual.

1: assemble/glue together the daggerboard trunk

2: cut off the the outsticking spacerparts, flush with the daggerboardtrunk

3: install/glue the case in the boat

The daggerboard is installed on the bottompanel, no parts are going through it.

Ruud

The extra length is deliberate.  When you glue and clamp the daggerboard trunk assembly together, the trunk spacers will slide around.  Without a little extra to trim off, you'd always end up with one or both spacers too short.