why should operable and inoperable be opposites if flammable and inflammable mean the same

The answer is in the roots, Zed. The 'in', in inflammable, is not a prefix. The word itself is derived from the Latin root, inflammare, which itself means to burn easily. Whereas, the 'in', in inoperable is a prefix, signifying 'not'. (I don't know the root for operable; our Latin guru, faldage, will check in in the morning I hope, with more on this)

Off the top of my head, I can think of two other such words wherein, the 'in' is not a prefix, but part of a root: inchoate and indict

Not always can we divide a word and conquer it, eh!