Correct.
I think they do take the linking into account when they do upgrades.
We have been upgraded twice, once from Cat 2 to Cat 1 (yes, that would be the Walt Disney Suite - I still can't believe it!) and another time from Cat 6 to Cat 4. In both cases, we were notified by our TA a week prior to the cruise, not at the pier.
On both cruises, upgrades were available at the pier, for a price which was cheaper than at booking. We met some people that paid to upgrade at the pier. At some point at sign went up that said 'Captain Mickey says the ship is full and there are no upgrades available'. I have also
heard that some people have gotten upgrades at the pier, but I haven't actually seen it or met anyone who got one of these.