Transferred points from a different use year do not show up in your online account even though you have them, and as a result you must call to make a reservation using such transferred points. Thus, the disadvantage is that you lose the ability to book online exactly 11 or 7 months out at 8 a.m., and instead must wait until 9, and that delay can for some room categories and times of year be deadly to getting the reservation.
If instead, you do separate reservations, you have the issue of two different 11 (or 7) month out issues, i.e., you use one use year to reserve some nights 11 months out and then have to wait those number of days to make the second reservation using the other use year, but you still reserve the 8 a.m. advantage for both. Moreover since you cannot mix the points from both use years to make any single night's reservation, you may have issues having enough points in one to get all the nights you want.
Thus both methods have their advantages and disadvantages. I have two use year's and personally never use the transfer method when I want to do a reservation using both use years, but instead make the two separate reservations and then send an email to MS to have the two reservations linked, which results in not having to change rooms. But I usually do it not because of the 8 a.m. to 9 a.m. issue, but instead because hold times on the phone waiting to speak to someone have become too long and because I often just make reservations late in the evening after MS is closed.