We have recently released a patch that allows these two fields to be applied to the .replit file:
# Stops the packager from installing packages when running the Repl
disableInstallBeforeRun = true
# Stops the packager from guessing and auto-installing packages, but it still runs to install packages when running the Repl
disableGuessImports = true
I was able to reproduce the issue and let the team know. I believe this is to do with our new Modules system that encapsulates configuration for languages such as Python onto our own infrastructure. This seems to prevent users from configuring the packager in the .replit file.
I will follow up once I have an update.