Having bought two new laptops recently, it's a mix. The Dell comes with a few partitions on their factory install. One is a FAT partition for their diagnostic tools, the other is for their Media Direct program on a FAT partition, a recovery partition on FAT, and lastly the actual OS partition which is NTFS.
The Acer I got had two partitions both were FAT which I thought was pretty ridiculous.
But like you've said, I alway do a fresh install to get rid of the bloatware. In the case of the Acer, the reinstall removed a security issue that was present with the factory install. An active X file would have allowed someone with a malicious website to launch stuff on your desktop without needing admin access.