@Peter - We have been working behind the scenes to investigate and publish a proper response on the transport agents issue. I am pleased to report that just a couple of hours ago we published a KB and a FixIt solution that customers who are having problems with transport extensibility via agents can use to correct this condition on their servers. The FixIt provides a script that customers can run directly or add to their deployment steps to resolve this issue. Details can be found in http://support.microsoft.com/kb/2938053.
To address your question on what impact modifications by customers who may have removed or modified the comment already on their server will encounter, the answer is there is no ill effect from doing this. These customers will have no problems using SP1 or moving to other later versions. The comment is there simply to identify the version of the file, typical action in software, and its absence will have no detrimental effect.