If I use the Windows 7 backup on a system that has the 63 sector starting location and restore it to an advanced format 4096 sector system, will the restore create the starting sector at 63 or 4096?
Windows 7's built-in backup tool works with files. Backup sets that it creates are on a file level, not a block level. That tool does not know or care about 512b vs 4K block size drives.
If you are restoring to an already properly formatted/aligned drive, then your data will be aligned. If you are restoring to a brand new drive with no partitions, then Windows Vista and newer create properly aligned partitions.
To verify what kind of disk you have, from an elevated privileges command prompt
A 4K Native Disk has the “Bytes Per Sector” and “Bytes Per Physical Sector” fields both set to 4096. A 4K Sector Disk with 512-byte Emulation has the “Bytes Per Sector” field set to 512 and the “Bytes Per Physical Sector” field set to 4096.
To see the status of your partition tables, from an elevated privileges command prompt run