I have a couple of ideas for you.
First, I would look at custom notifications. You can write a simple .NET assembly to implement your custom email code and then in workspace execute a method in this assembly in response to many different events. This allows you to administratively configure the emails without re-deploying the workflow. I have a very simple example of a custom notification I can send you if you need it.
Second, there is a whitepaper on our customer portal on how to create your own wizard that you can add to the Visual Studio toolbox in the workflow designer. It's straightforward, but a little more difficult than creating the custom notification. This would allow you to drag your custom event on to the design canvas whenever you need it.
Lastly, yes, you can change the default code for the mail event. Although very easy, I would save this as a last resort. When we deliver any future service packs, your changes to the template would likely be overwritten. You would have to make a copy (always a good idea) and then put your copy back after the service pack. Also, if you make a change to a template and introduce a bug, it would be difficult for our helpdesk to figure out. If you locate the whitepaper on how to create your own wizard, it will be obvious how the code templates work and how you can change the OOTB templates. If you want more info on this, send me an email.
David
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