Most often it's because the online systems reflect what is currently available to all subscribers (new and old). Any grandfathered packages or bundles will vary from one subscriber to another, and not everyone will have the same tiers.
By calling in (as painful as it is sometimes), you can ask, ask and ask about what you can do (before they do it) and ask again that "if I do this, will I lose that?" If they say "yes, that's right", then ask again just to confirm "so - I have the HD Value pkg and want to add this HD bundle - I'll keep the others, right?"
Personally, I can't speak to any of the "horror" stories with regards to the Bell CSRs because everytime I have ever called, I did not have any problems. When I first moved to HD, my first month's bill WAS all screwed up, and I didn't get my programming and rental discounts. I immediately called and had it corrected in minutes.
Unless I'm checking my bill, or seeing what other bundles are available, I simply don't use the self serve website.