Thanks for the reply. I think the easiest thing is to refer to one of the public examples out there which you have picked out which demonstrates the issue. Your 2) example is perfect.
https://jjallaire.shinyapps.io/shiny-biclust/
The view source shows the HTML for the initial loading screen. Not the actual website itself. (This actual code (as you know) is found through developer tools and Elements).
So as far as I can tell, the trick is how to customise Rmarkdown source files which create this intial loading HTML code as that is all google web crawlers see.
I'm concentrating on trying to find this in source
<div id="rmd_loader_wrapper">
<div id="rmd_loader" style="display: none">
<img src="rmd_resources/rmd_loader.gif"/>
<p>Loading</p>
</div>
</div>
I can find the gif and a bit of js in my local library install ...rmarkdown/rmd/h/rmarkdown
Online this https://github.com/rstudio/rmarkdown/blob/master/R/shiny.R file at line 351 has "Please wait" instead of "Loading" as the text. But I can't find anything remotely like this in my local files. As I have no shiny.R file in my local files that I can see on windows.
I think this is an interesting issue for any flexdashboard developer.