As noted above, full hardware access isn't really possible with any virtualization technology for commodity hardware. What you might want to look into is LVM on Linux. LVM2 includes support for read/write snapshots. In essence you can create your clean install, take a snapshot, and use the snapshot as your filesystem. LVM2 snapshots only require extra storage for blocks changed after the snapshot, so your base install would still provide (hopefully) a majority of your actual running OS. If/when something gets borked, you can restore to your clean install, create a new snapshot and go from there.
As an added bonus, you could (with enough space) create multiple snapshots and maintain several different versions of your OS.
Most modern, popular Linux distributions are capable of using LVM at install time. For Ubuntu it is an option, for Fedora it is the default.