It might be helpful if the functionality we copied over to Ark for tool calls in Positron was implemented in base-R only standalone files. This way the functionality is updated and tested in one place, usethis can be used to manage updates (https://usethis.r-lib.org/reference/use_standalone.html), and we wouldn't need to adapt the code to base R when we need to update.
You can see which functions we adapted in posit-dev/ark#868 (file pandoc.R).
This is just a suggestion, I'd understand if you think this would be impractical or too constraining on your end.