If you are getting an UK Tier 2 (General) visa and have British National (Overseas) status, you should get your UK Tier 2 visa using your BN(O) passport. This is because -
1) BN(O) passport holders with a long term UK visa do not need to register with the local police while HKSAR passport holders, as Chinese nationals, are required to register with the local police.
2) BN(O) passport holders with long term UK visas are treated as Commonwealth citizens in the UK. He/She can register to vote in all UK elections. HKSAR passport holders cannot register to vote in any UK elections. Being on the electoral roll helps you to build up your own credit history in the UK.
3) BN(O) passport holders can apply for British civil service jobs open to Commonwealth citizens once he/she has Indefinite Leave to Remain (ILR) while HKSAR passport holders cannot apply for British civil service jobs until he/she has become a British Citizen.
4) BN(O) passport holders can apply for registration to become a British Citizen using form B(OTA), this is a cheaper method than naturalisation. HKSAR passport holder must naturalise in order to get British Citizenship.
https://www.gov.uk/government/publications/application-to-register-as-a-british-citizen-form-bota