The bash script and C# application uploads the current Hashrate, Accepted, Rejected Shares, and while doing do fetches the pool address it needs to connect your miners, this makes it very easy for you to switch pool for instance if a pool goes down.
Also the bash script and C# application makes sure that your miner is always up and running, for instance the bash script tests if the load is above 95 percentage and temperature is below 85, if receding these thresholds it will stop the miner temporarily, and you will get a notification by email or SMS. after 2 minutes it will restart the miner again.
If you are concerned about miners being "remote controlled", you can always stick to Pool statistics via API token's or simply disable this in the scripts.
But you are right in your concerns, I can only show my honesty by running a great monitor.
You might want to consider a donation/fee based app that people can run on their own servers with code that can be audited for security.... otherwise how do we know what is going on behind the scenes?
I might consider that in the near future. Regarding security audit, you can always purchase my pool script and see how I code.