I can't speak directly for Honda because I haven't worked for them (I have toured East Liberty, Anna, and Marysville multiple times though) But, I have worked in auto manufacturing for a few years. The vast majority of the marks and tags you find on a production vehicle are just an artifact of process and quality tracking during assembly.
The tags, especially the scannables, can be used to assign a finished QC passed part to an internal production database that (at least for my company) would be mothballed until a quality issue was found. We would also use the tags to track rejects and produce quality documents to track individual parts trough production automatically. At a full car assembly level, individual parts are digitally assigned to the car so it can be identified in a recall or TSB situation.
The hand written marks can vary greatly. Some are simply verification of some visual part check will change as quality issues are discovered or mitigated. Some are just a bored intern doodling on hidden portions of parts
So I guess the point I'm getting at is that I wouldn't put a lot of stock into the random marks you find throughout a car. The vast majority of them are inconsequential.
This is an awesome thread though. It's nice to see people wanting to dig more into the history of Honda production. Production is a really neat thing if you geek out on statistics and efficiency.