Currently the goal of the EmailReporting plugin is only processing the incoming email.

If people answer inline then the reply part of the email should not be removed in the first place.

As for any modifications in the notification system. I feel that should a separate plugin that depends on EmailReporting if you so wish

I agree with you. Initially, I thought of a different plugin, but the inline reply part put me back to the ER plugin. But since you suggest a new plugin, then it's the way to go.

AFAIK, there are no events available to customise the mail content. So this cannot be achieved immediately.

I'm going to keep this issue open. Maybe i'll think of something that could facilitate this feature.

You can make plugins optionally depend on another plugin and plugins can check whether other plugins are present and if so do something

Though the biggest issue is that, to my knowledge, we do not have any plugin events available that would allow us to modify email content

If this does become possible one would only need to add the following code to check whether emailreporting is currently processing an email

if function_exists( 'ERP_get_mailbox_api_name' )
{
$t_mailbox_api = ERP_get_mailbox_api_name;
if ( isset( $GLOBALS[ $t_mailbox_api ) ) echo 'ERP active';
}

or something like that...

Cas created a code that might help. But it requires code editing because, like you said, there is not option to change using a normal plugin.
https://github.com/mantisbt-plugins/mailtemplate

Since this is out-of-scope i will close this issue