Let me answer your questions.
1. You cannot manually generate the ID during MSI configuration because the output file is supposed to be used multiple times. Whereas the ID is a unique number/code.
So you either select the "Generate ID and send it via email" option, or get/generate the ID manually in the Host settings after the Host is installed.
2. If you are selecting the "Standard MSI" option, and launch the output file - the installation will look like a regular installation, with all installation wizard windows including the "set password" window. To silently install the program with all the settings you need use the "One-click" installer.
3. It has something to do with either firewall or spam filter in your inbox. Please ,check this KB article https://www.remoteutilities.com/support/kb/e-mail-is-not-sent-error/
Hope that helps.