I'm thinking they are prepped\protected in some way
No, they aren't - they are just stock-standard WIMs built by ImageX with no particular trickery.
The only unusual thing about the WIMs at all is that there are two combined, one WinPE-256 for low-memory systems, with all kinds of drivers and optional subsystems disabled to fit - editing this one is generally a bad idea since memory is too tight to add much to it - and WinPE-512 for normal systems.
You can build a combined WIM pair for yourself from scratch using a process like http://blogs.technet.com/b/cameronk/archive/2010/04/29/consolidating-your-task-sequence-part-1-how-to-combine-wim-images-into-one.aspx
Known bugs in the "mount" functionality of ImageX is not something I can speak much to, as I never used it and in particular the Ghost Boot Wizard didn't use it either - the main reason for that was that the "mount" option wasn't available on some of our supported platforms at the time, but there are a couple of subtle things that don't work well with ImageX when you mount/unmount WIM images.
The main difference between mount-style editing and the regular ImageX capture is that different compression algorithms are employed; things added to a mounted image are compressed using a low-compression algorithm, used only in ImageX and patented (not for any good reason, it's not an innovative or interesting algorithm) called Express. Also, you don't get single-instancing with mounted images.
As a result, mounted WIM images don't compress very well, you lose most of the advantages of ImageX's single-instancing, and there are platform restrictions which mean you can't always mount anyway.
That's why to edit the WIM files, the Ghost Boot Wizard actually goes through the process of unpacking the sub-image within a WIM and re-packing it again using ImageX so that the high compression options and single-instancing work, and it can run on every supported platform. That process is just more reliable, and gives a much better result especially given that for lots of purposes like PXE boot the raw WIM size does matter.