If I need my ‘trust licence’ for certain things in the world of commerce for applying for things, do I just use my RRDJ certificate and will it be accepted?

No,  the identification documents supplied by the gov corp machine are useful to travel in their system.   So use whatever they provide if it suits you.. however, because they are the registry in their  world as we are in ours they make the rules… the lord giveth and the lord taketh away.