I'll start from the end and work my way back.
Enterprise Transporter is used to consolidate BlackBerry Domains. That said,
"The BlackBerry Enterprise Transporter does not support moving BlackBerry smartphone users from one messaging platform to another (for example, from an IBM® Lotus® Domino® environment to a Microsoft® Exchange environment)" ... moving from one Exchange Org to another Exchange Org, from the BES perspective is exactly this. Enterprise Transporter is technically only supported when migrating TO 5.0 not from sub-version to sub-version ... that said, as long as the other requirements are met I'm pretty sure it'll work (I haven't validated this yet though).
The boundary for BES is the Exchange Org; it cannot span multiple Exchange Orgs, nor can it move from one Exchange Org to another without a complete reinstallation ... just as a forest is a virtual boundary for Exchange.
If Exchange 2007 had been installed in the same Exchange Org as the Exchange 2003 server you would have been able to do just move users ... and possibly even use the transporter suite. (InterOrg migrations are NOT supported with BES ... As an FYI here is what happens from an Exchange perspective
ExchangeIS : AD and Exchange InterOrg Migration - A Real World Example Part 1)
In a scenario with over 1000 users (frankly in just about ANY scenario), the Exchange 2007 should have been installed in the same Exchange Org as the already existing Exchange 2003 servers and then a simple mailbox-move could have been performed on any users. The same GAL would have been maintained and the transition would have been simple. I've only done what you have done once, and it was against my better judgement; but a requirement of the client ... who didn't have a BES.