I would not export to CSV file, but would use a mongodb csv exporter script right as a csvpipe_command in your config, just to avoid unnecessary write/read, but it should would with files as well.
Not sure why you want to modify your config multiple times. Just prepare your config once specifying there all your plain and RT indexes and then attach the plain ones to the RT indexes in a loop.
Also since you are going to have RT indexes in the end I assume you are going to write directly to them along with mongo (or instead of mongo). If it’s not the case (and you want to keep syncing from mongo to manticore) then just plain indexes may be ok and main+delta schema may be more beneficial. We have an interactive course about it Manticore Search - Main+delta schema