Ideally, yes! But some trans men (after a long time on testosterone) have beards, noticeable male pattern balding, and deep voices, so may alarm women if they use the women's toilets. The recent Supreme Court ruling on the Equality Act 2010, specifically references this potential problem.
The large majority of trans women are very obviously male (from a woman's perspective), so I agree their use of the men's toilets should be encouraged. But men seem, on average, much less able to 'spot' a trans woman. And if I were a man I would hate an apparently female colleague to see me using a urinal. Mortifying!
It IS an awkward, imperfect compromise. But we should probably consider allowing - on a specific site basis - both trans men and trans women to choose either the toilet for their own biological sex or the gender neutral/disabled facility.
We will need to monitor the impact on all users, to check, of course, that this is working for everyone. It may need to become standard to have toilets that are: Men's, Women's, Disabled and a separate Gender Neutral self-enclosed room.
But that's for a possible future change to building/major refit regulations!