Respecting custom repositories files in interactive/batch R sessions

I may be missing something here but aren't you overcomplicating things?  One
can avoid the repetitive dialog by setting   options(repos)   accordingly,
and I have long done so.  The Debian (and hence Ubuntu and other derivatives)
package does so via the Rprofile.site I ship.  See e.g. here

 https://sources.debian.org/src/r-base/4.2.1-2/debian/Rprofile.site/

I have used the same mechanism to point to intra-company repositories, easily
a decade or so ago. I had no problems with R CMD check of in-house packages
using this.

Dirk

dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org