Just so we're clear, they send you a source file to compile as part of your assembly? Compiling in VS.NET is simply compiling the codebehind files. This is why I say in v2.0 if you don't want an ASPX or ASCX to be part of your application, then it shouldn't be there in the first place.
Well, only one of the files needs to be included into my solution and modified as I see fit, and compiled as part of my solution. The rest of the files are NOT to be included, they have their own DLL sitting in the BIN folder, and have their content encrypted / encoded making them difficult to view / change etc...
I don't know enough about this product to offer an opinion about how they're doing things. But, it does sound like a vendor issue. This is going to be a problem for every one of their customers, so they're going to have to come up with a solution. I'd contact their customer support and ask them when they plan to have a fix.
Yes, I've informed them of my talks with Microsoft, and they are working on the fix as we speak. Also, MS has not ruled out having this feature completely removed (http://lab.msdn.microsoft.com/productfeedback/viewfeedback.aspx?feedbackid=84ab7f2f-bdcd-4e66-acaa-8c57dc016254) All those who would like to have this feature brought back, please go and VOTE on this issue! The problem from MS point of view is the project file. I believe we have a suggested workaround. Go VOTE so MS will take this issue seriously!