How does a hard drive knows what bit is the beginning of of a byte/word?
Simplified, the operating system sees disk storage as a randomly accessible set of sectors, each sector containing some fixed number of bytes.  The OS asks the disk controller for a sector using some standard protocol and it is the responsibility of the disk controller to retrieve the sector with the bits and bytes in the same order in which they were written.  The communication protocol (e.g. SCSI) specifies both bit and byte order for reads and writes so there is no space for confusion about where the data starts and stops.

Operating systems can and do take into account the characteristics of storage media for the sake of efficiency, such as existence of onboard cache, rotational delays, and head movement, but those things have no bearing on where bytes and sectors start.