Intrasex runners were considered to be women so there was no transition was involved; they were not giving a world class career as a guy to run as woman. I believe that they will no longer be able to run without testosterone suppression?
The problem is that for a world class male runner doing so is not practical. They're going to have to sit out for a year and there is no guarantee how competitive they will run as a woman. Yeah, only transphobes will hate them but being booed at meets having high profile people and politicians taking shots at you on Twitter is going to be unpleasant. Waiting until my competitive career was over to transgender would be an easy decision for me. Running 3:55 is a fantastic time and it must be a rush to run that fast. There's no way I would trade that for a 4:25.
They're is no example of your average guy becoming a champion as a female. Eastwood was at almost exactly the same competitive level as a male and as a female. I believe her HS times were consistent with what she did in college. We can't read her mind so we don't know if she expected to become a 1500 NCAA champion as a woman.
The Connecticut sprinters could run without treatment so an average male could be a champion as a female in that scenario but they won't be able to do that as a NCAA or professional athlete. They also weren't eligible for scholarships.
What would be the path for a transgender female to be a champion at the NCAA level? It would probably require a HS boy with 8:50 talent. There are no drug treatments so does he run that time as a male and then risk his scholarship by transgendering in college or as a girl and not receive a scholarship out of HS. Considering that the person has about 60+ years remaining in his/her life, waiting a few years to transition is the easy decision.
In your cyclist example, you say "he" already has the Olympic qualifying. Were those times achieved after testosterone suppression treatments? If not, she hasn't qualified.
You're last paragraph moves away from the discussion of transgender competing against women. I'm not a proponent of MTF athletes competing but it's been settled in court. I'm confident the rules in place will prevent there ever being one competing at a high level of any sport that I care about. It's unlikely a professional female distance runner will ever compete against a transgender female so none will have to rollover to accommodate guys.