Two completely separate backup schemes are needed here. One for full "cold-metal" restores of the boot/OS level stuff, and IMO this is best done with "imaging" style software, in your case specifically targeted for windoze/ntfs systems. These don't need to be done very frequently, as little is changing from day to day. BPC is not intended to provide for this kind of backup, especially regarding Windows. Many Linux sysadmins simply re-install their OS from automated scripts and then restore config files rather than bothering to fully image their boot/OS partitions, but Windows isn't suited to that approach.
The type of backup is for working data, which requires the frequent full/incremental/archive that BPC is designed for. Details about the infrastructure "under" the filesystem are irrelevant to BPC, except when considering how to optimize performance when a small "backup window" becomes an issue. What you are doing with LVM snapshotting should only be necessary for certain applications that keep their files open, like DB servers, Outlook and some FOSS mailsystems. And then only if these services need to be kept running as close to 24/7 as possible, otherwise your scripts can just close the server processes down until the backup is complete and then bring them back up again. I can't advise on the NTFS-specific extended attributes and newfangled security stuff, but unless you're using software that specifically leverages that MS-proprietary stuff, it shouldn't IMO be an issue.
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