Even granting your distinction, the exact same argument still applies: just substitute in an additional rate of, say, 10% chance of going from replication to whatever you choose to define as 'success'. You cannot say that a 11% replication rate and then a 1.1% success rate is optimal - or suboptimal - without doing more intellectual work!
No, I don't think so. An 11% replication rate means that 89% of the published results are junk and external observers have no problems seeing that. Which implies that if those who published it were a bit more honest/critical/responsible, they should have been able to do a better job of controlling for the effects which lead them to think there's statistical significance when in fact there's none.
If the prior odds are 1:10,000 you have no business publishing results at 0.05 confidence level.
For those who haven't heard, NIH and NSF are no longer processing grants, leading to many negative downstream effects.
I've been directing my attention elsewhere lately and don't have anything informative to say about this. However, my uninformed intuition is that people who care about effective altruism (research in general, infrastructure development, X-risk mitigation, life-extension...basically everything, actually) or have transhumanist leanings should be very concerned.
The consequences have already been pretty disastrous. To provide just one, immediate example, the article says that the Center for Disease Control and Prevention has shut down. I think that this is almost certain to directly cause a nontrivial number of deaths. Each additional day that this continues could have huge negative impact down the line, perhaps delaying some key future discoveries by years. This event *might* be a small window of opportunity to prevent a lot of harm very cheaply.
So the question is:
1) Can we do anything to remedy the situation?
2) If so, is it worth doing it? (Opportunity costs, etc)