We cannot truly know someone's intent. We can evaluate the impact of their words and actions. If you define words like “racist” and “transphobic” to be solely about professed intent, then you will find that bigotry seemingly doesn't exist.
Anyway, you have to really stretch it beyond reason to see transphobia behind anything RMS has said, written, or done.
As for the impact of his works and actions, everyone has access to a full software stack to explore, learn from, and work on, without the need to be inside some university or company, i.e. to have the money or to pass admission processes that might be putting certain groups at a disadvantage, or outright excluding them. This was also his intent all along and he sacrificed a lot for it.
Oh, you can get pretty close. What you do is you look at their attitudes towards the marginalized individuals, to marginalized communities, their opinions as a whole, their advocacy, their friendship groups, etc.
If, on balance, they appear to support and promote people of colour or transgender people (as much as they do any other people group) - then this person is probably not racist or transphobic.
However, that's haaarrrd. And doing that groundwork doesn't win you clicks as a media outlet. Whipping up a mob does win you clicks however. And advertising revenue.
And then many people - who have only read those articles - shout about it, like mobs tend to do, it seems like it has universal approval, and people assume it's probably true.
If you don't define words like "racist" and "transphobic" to be solely about intent, those words become meaningless.
Is the purpose of the electric car to make CO2? Of course not. Yet for a long time (not sure whether this has changed yet) more CO2 was wasted in their production and transport than they could ever hope to save in over 10 years of operation.
Is your purpose to make blaisé, ill-thought-out over-generalisations on the internet? Of course not. I imagine you lead a full and fulfilling life offline, spoiling orphaned kittens rotten and brokering peace treaties in your spare time.
Just because a person (or, if you prefer, a system) produces an unintended side effect - whether by accident, ignorance or bad publicity - it does not make that their purpose, or even reflective of the kindness in their core being.
And sometimes, these things can be fixed with education. Sometimes these things can be fixed with holistic reporting and good PR. Sometimes, other people need to learn to do their own research to understand and accept the context in which things are said.
But alas, the internet will never learn these things. Because the purpose of a system is what it does - and what the internet does really well is spread hate and division.