Pointing out that biochemistry couldn't be the same if water was different sounds like deliberately missing the point of Putnam's experiment. Suppose a planet like Earth, but where most people are left-handed, have their heart in the right-hand side of their body, wear wedding rings on their right hand, most live in the hemisphere where shadows move counterclockwise, most screws are left-handed, conservative political parties traditionally sit in the left-hand side of assemblies, etc., etc., and they speak a language identical to English except that left means ‘right’, right means ‘left’, clockwise means ‘counterclockwise’, etc. (Throughout this post, I use upright type for actual English and italic type for the language of that planet.) BTW, they are made of the same kind of matter as us, so that in their language lepton does mean ‘lepton’, antilepton means ‘antilepton’, etc. Now, when someone on that planet (who's not a particle physicist) says left he's thinking the same thoughts as someone on this planet saying ‘left’, but it doesn't follow that left in their language means the same as ‘left’ in our language (because the statement in their language only right-handed leptons and left-handed antileptons participate in the weak interaction is true, but the statement in our language “only right-handed leptons and left-handed antileptons participate in the weak interaction” is false)... or does it?
Bar pbhyq nethr gung vs fbzrbar vf abg n cnegvpyr culfvpvfg gurve ynathntr qbrfa'g npghnyyl unir n jbeq sbe yrcgba rgp. Ohg vs jr tb gbb sne qbja guvf ebnq, gur vzcyvpngvba vf gung vs V gryy fbzrbar gb ghea yrsg, gura vs gurl qba'g xabj nobhg cnevgl ivbyngvba va jrnx vagrenpgvbaf jung V zrna ol ‘yrsg’ vf abg jung gurl zrna ol ‘yrsg’, juvpu frrzf hafngvfsnpgbel gb zr orpnhfr nsgre nyy gurl qb raq hc gheavat jurer V jnagrq gurz gb ghea.
Well, 'left' means 'right' and 'right' means 'left', right? That their macroscopic world is a parity-inverted copy of ours (and that their word for 'left' souds the same as our word for 'right') is an unfortunate confusing accident, but I don't see how it would justify translating 'left' as 'left'. The representation of 'left' in their brains is not the same as the representation of 'left' in our brains, as demonstrated by different reactions to same sensory inputs. If you show the twin-earther your left hand they would say "it's your right hand". In the H2O-XYZ counterfactual the mental representations could be the same, thus Putnam's experiment is different from yours.
Thagard (2012) contains a nicely compact passage on thought experiments: