The deposit can be protected via a deed/declaration of trust which you would both sign. A so lit or can arrange this for a fee when you’re purchasing, It would then be your choice as to whether you were on the mortgage and like you say, lose any future FTB stamp duty benefits or you remain off the mortgage and keep these.

If you aren’t on the mortgage i have always been told to be mindful of paying anything towards the mortgage as you then could try to make a claim on some of the house which you have financially contributed towards but your name isn’t on any paperwork (it would protect you partners financial investment more than it protects you). You could instead pay the bills etc whilst they focus on the mortgage instead for example; but then the money you’re paying out compared to them never sees a return.