We have two use years, with the second purchased about 20 years ago. Over the years we have made many reservations for the same room size/view at the same resort, reserving some nights with one use year and the rest with the other. On every occasion, we contacted MS and had the reservations linked. We have never had to change rooms.
For the years before they had an online reservation system, we also never had to do anything special at the front desk, such as doing a pseudo check out/check in on the turnover day, except to mention both reservations when we checked in. After the online reservation system started (can't remember exactly when but about 2012), we started to have do that pseudo check out/check in on the turnover day. We were informed at the time that was because the newly created computer system would not allow recognition of the two reservations as one continuous reservation. Since 2015, we have no longer needed to do that and were informed at the time that the computer system was updated to recognize the separate reservations as one continuous reservation when at the resort as long as they were linked in the system, Thus, since then, we have had to do nothing at all, other than to originally link the reservations when made. to assure we kept the same room.
As to MS mentioning that it could not guarantee we would avoid changing rooms, the last time that was mentioned to me was in 2013. In the last three years, I was actually told twice that linking the reservations now assures you will not have to change rooms or do any check-out/check-in on the turnover date. Maybe others are still being told otherwise and possibly some are doing that turnover date activity, but it certainly has not been our experience.
What you cannot do is buy the dining plan for one part of the trip and not the other if you link the reservations. To do that, you cannot link the reservations and will not have any assurance of remaining in the same room.