In the current version of Omnifactory(v 1.1.0) doesn't support the GTCE dusts (tiny -> small -> dust) conversion in compacting drawer. Is this intentional?

Yes, GTCE dust conversion doesn't used shapeless recipes, it uses shaped recipes instead, and really it would only be able to do tiny / dusts, and small dusts would get left out altogether if it was implemented to fit with compacting drawers.

Intended solution is to use the Packager or just automated patterns in ME system.

Understood and thanks for the solution as well!