The only time you would see the phrase 'Offer your reply' is when you go directly to that superdoc, which is something you shouldn't do, so that's that. Same goes for 'Comment on'.

The result I believe is confusing for people new to the site as the phrase 'Comment on' seems to imply (to me) that you wish to bring something to the attention of the 'powers that be' rather than 'reply' which, of course is self explanatory.

WOW! That is just incorrect (there are no such implications).

Presumably there is/was a different purpose for the two areas but it's difficult for a lay person to see what that might be.

Huh? You click on the correct link to respond to what you wish to respond to, and that's that. All the other details are of no consequence.

While on the subject of 'reply', when I click 'reply' I would prefer to view the whole thread that has gone before rather than just the message that I am replying to.

When you wish to respond to a node, simply open the "comment on" (or "reply") link in a new window, while retaining your old one with the entire thread in it (low tech rules).