Behavior differences between R from command line and RStudio

Error Information:

Not really an error, more an information request wrt the scope of RStudio's startup differences from R running from the command line.

Description of issue -

RStudio has been adding extra bits to the environment of a running RStudio session for a while now. Whether that is for loading/interaction with the rstudioapi or initializing behavior with Repositories, there seems to be no guarantee that code developed in RStudio will work identically in a standalone R process.

I've noticed as of RStudio Server 1.2.1335 that RStudio will impose logic based on the nature of the repos that have been selected.

This appears to result in scenarios which might be reproducible under Rstudio but not under R from the command line here or here.

Many configuration steps seem to have a significant GUI component. (Which is problematic when you have 40-50 users and you don't want to walk each one of them through the gui)

My Questions are:

What is the scope of RStudio's startup changes? Is there a good way to test that code will successfully run under an RStudio startup from the command line?

Can all GUI configuration elements be configured globally from some global config somewhere?

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