No, you cannot create Package Manager packets, which your device would accept. "Services -> Package Manager" functionality is only mean to allow install official Teltonika packages.
The proper way to transfer your script to the router is either through SCP protocol as a file, or through SSH as a plain text (by creating new file on the router and copy-pasting its text over SSH). I seems that you are familiar with both of these approaches already.
If you want to simplify this process and make it easier to upload or update your script in the future, you could either make changes to your script, so that it would attempt to connect to your servers and update itself remotely, or you could implement any third party "package manager" alternative, which are meant to share generic files/packages.
Additionally, take note that you can compile your own custom firmware, with your script already built in the firmware. If update would ever be needed, you would be able to simply compile new device's firmware with new version of your script. SDK and its brief instructions can be found here:
Meanwhile, it does not matter where you would place your own script files on the router (that should not interfere with the device). You can place your script in /bin or /usr/bin directories, since these directories already have prebuilt binaries.