As in "For choice, I'll eat coxes, but other kinds of apple will do", yes?
It is an odd phrase, but it's not unfamiliar to me (in the UK). It seems much less formal to me than "by choice", but synonymous with it.
If it were "For my choice",I can't think of any particular origin for it would be regular, so my speculation is that it is a contraction of thator reason for "for" rather than "by". I don't know its origin thoughBut idioms often have idiosyncratic prepositions: consider another phrase which means much the same "to my mind". Why "to"?