Hi Steve!
1. First of all I would invite you to read MS CRM 4.0 Implementation Guide very carefully, specially sections 4-47 to 4-51. Also check section 3-29 of the Installing Guide (part of the Implementation Guide). There you can read that "The e-mail router is required for users or queues that do not use Microsoft Dynamics CRM for Outlook". What does this mean? If your user's use MS CRM for Outlook client you don't need to set up the E-mail router or any forward mailbox for them. The Outlook client is smart enough to promote CRM related e-mails to the CRM server. The router enables you to promote e-mail messages to the CRM even if you're not using the MS Dynamics CRM for Outlook client. I'm using it to retrieve e-mails for my CRM Queues. The router is not required if you use the Outlook client.
2. MS CRM doesn't do anything to your Exchange. MS Dynamics CRM clients for Outlook retrieve e-mails from your user's mailboxes and promote them to your CRM server while CRM E-mail router does something similar but whithour user intervention. You don't even need to install any CRM component on your Exchange servers.
3. Regarding your server configuration I don't seem to understand the problem because MS CRM will retrieve e-mail from your user's mailboxes wherever they are (don't care about the server) and the E-mail router if used will also retrieve e-mail from a mailbox wherever it is (you just need to configure one or more server connection). So I'm guessing it won't cause a problem with your CRM.
Regards,
Sergio Coelho