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I am working on a ROM mask chip, so I want to put Filesystem on EEPROM. However, I am not sure where I can start my Filesystem. Can I just start it right at the beginning address of EEPROM?
When the economic incentives are large, and the bad guys aren't able to reprogram a flash-based chip, then the bad guys will instead replace the box with an identical-looking box with other electronics.
In the end, physical access to the hardware will always represent a big security issue whatever chip is used.
Anyway - I would normally not use any file system for the type of information you want to store in the EEPROM. It's easier to just preallocate different regions of the EEPROM for different data and then store records of data of different type in the different regions. Preferably complete with good checksum information and redundant storage so the software can handle failed writes (such as after a power loss during save) or broken memory cells. Also with enough spare record space to allow wear leveling by not writing to the same addresses constantly.
So you might have a ring buffer structure for each individual type of information and on each write rotate through the available record positions while using some sequence information to know where the most recent entry is stored.