Chris: I can give you that information, however Yamaha does not recommend ever modifying your instruments.
Me: Well, that's kind of weird, because EVERYONE (ok, not really everyone) mods their instruments to some extent.
Chris: Anytime you do any kind of modifications, you could damage your instrument.
Me: You realize that you have endorsed artists that take your instruments and drop in Dimarzio, Hipshot, Gotoh, etc. parts, right??
Chris: ... however Yamaha does not recommend ever modifying your instruments
You (in a better timeline): Yes, I'm experienced with that sort of stuff and am aware of the risk. Please give me the information.
I don't understand why you would go into lengthy rant/discussion about how others modify their instrument and how it is common practice. Chris was so obviously just following a script and you seemed to know that as well.
Moreover, Chris is most likely not a guitar tech and just a general customer service agent that will direct you to specific departments (as he did later). The discussion about details in pickguard-changing after the non-recommendation is not productive at all. I wouldn't expect the first person I call at Yamaha to have a discussion with me about that, and certainly wouldn't initiate such a discussion either since it just doesn't make sense. With the person from parts department maybe, but not with Chris. Leave poor Chris alone, dude.