The only way the FGS could sideline Puntland is to block it from receiving its share of international aid.
This would mean that Somaliland, which has declared secession from Somalia, gets better treatment from the FGS than Puntland which is anti secession. Somaliland has a longstanding deal with the FGS where it receives it share of aid directly. Over the past 10 years, HSM and Farmaajo have rarely fucked with this setup. However, they have often punished Puntland for its political decisions by refusing to authorize various aid projects. A secessionist state gets better treatment than the state that refused to secede and helped setup the central gov.
Also, the quality of institution created by the federal government will always be lower than if Puntland had itself created its own local versions. The levels of corruption in the south will always be higher than in Puntland, and the staffing of these federal institutions will always be based on 4.5 not on merit.
You are asking Puntland to do things that would lock in slow political and economic development out of pure spite.