2. If it's true that the difference in spatial reasoning is due to social factors as the priming study suggests, then you might expect trans people to perform like the sex they were born as since they were raised with that set of gender stereotypes before they transitioned (although this might additionally be modulated by how long they've been living as their true gender). And with the priminf stuff I don't know whether there are any predictions we can derive since so many things could happen. Having someone imagine themselves being the gender they were born as probably isn't a good experience for many trans people so you might expect both groups of trans peopls to be worse, or maybe it doesn't affect them negatively and you expect the same pattern of results as in the original study. It's hard to say and I don't think any experiments have been done.

3. This is why science is about population averages, not individuals. It's great you've never felt this way but it doesn't mean that on average various minorities don't feel this way. These feelings are going to be somewhat normally distributed and you just so happen to be on the tail. Or so you think - you can't predict how you would actually behave in an experiment. This is why we do psychology experiments, our introspection isn't always right and many things are subconscious!

4. Interesting! Do you have a link to that study? The original study has been replicates so many times and one counterexample could very well be a false negative.