Windows not understand partition table format used in PS3 (let's call it PS3PT, it have not any official name). So for him, PS3 disks always be treating like empty. That's one of the reason why application like PS3 HDD Reader has been written. Initialization in Windows means writing MBR or GPT partition table, overwriting PS3PT and making Your life very hard in the process if You value Your data. PS3 not understand anything else than PS3PT for internal drive. Changing partition tables will not adopt partitions from earlier partition table. So You can now answer to Your question.
Anyway, logic structure on PS3 HDD looks like that there are so called regions (that's official name, but technically they are partitions). Each region (partition) can be separate device. So partition with VFLASH contain its own partition table and partitions, and partition with OtherOS have also its own partition table and partitions.
Main regions: user partition (mounted on PS3 as dev_hdd0), cache partition (mounted on PS3 as dev_hdd1), vflash (only on NOR models), otheros (only on fw up to and include 3.16 if user create one, and only on cfw with otheros++ if user create one).
- Cache using FAT32.
- User partition using UFS2.
- VFLASH sub-partitions using FAT16, FAT32 (mounted as dev_flash, dev_flash2, dev_flash3), raw without any fs
- OOS is the same as PC, so i.e sub-partitions with EXT4 or whatever, lies on MBR partition table.
Each region is encrypted, vflash twice, otheros probably also twice but how it is done is unknown yet.