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I work as a nutritionist and personal trainer...have for years. I've worked with transgender clients...they don't like the bio-impedence scales that tell bodyfat, muscle mass, bone density etc.

I've had to tell Trans women that we have to run them as a man on the scale otherwise their numbers would be incredibly skewed. For instance running a Trans "woman" would result in their bodyfats being tripled, yet the "man" setting obviously comes up very accurate...because they are biologically Men. Does that make me transphobic, or shall I lie to them just to make them feel better?

Why would you think that I think you're transphobic for telling the truth? I don't. What I also believe is that in any case you should tell the truth, as you see it, in a manner that shows consideration for the woman trapped in a man's body. I'm no medical expert, but I believe that for a biological transition to the opposite sex, it's necessary to start with puberty-blockers at an early age, followed by a sex-change operation at an age where the subject can make a responsible decision, before taking that irreversible step. Transgender women who haven't taken those steps will have to accept that they live in a man's body, and follow your nutritional advice. But the best way to make them accept your advice is by making them feel like you're on their side, that you accept they'd rather be treated like a lady, regardless of the hard biological facts. So, don't lie. Be honest and considerate. That's my amateur advice.

Bigoted
having strong, unreasonable beliefs, and disliking other people who have different beliefs or a different way of life

https://dictionary.cambridge.org/dictionary/english/bigoted

So by the contents of your own post,, you are in ,fact, a bigot .
Reconcile.
....learn more, type less.