Okay, so if they had their own space where only other transwomen could go, for example, how would it be any less safe than a women-only facility? It would give them the exact same protections.
If by privacy, you mean that it would out them as being trans, well in most cases, that would be obvious anyway, and if not maybe they need to get some therapy so they can feel good about who they are?
if you think that it might signpost them as trans to violent men who might enter the toilets to assault them, well that's exactly what women are worried about when it comes to letting transwomen into their own facilities, so it would be rather hypocritical.
Edit: This was in reply to @PiggleToes