YR,
Once this is posted you will see what I wrote earlier to you, offering to correspond with you directly if the Mods can facilitate that.
According to our Mesorah, the Alter Rebbe was instructed to write SA HaRav for the benefit of ALL Chassidim, and therefore Minhag Chabad is usually not included in his Psokim, as anyone familiar with Minhag Chabad can attest to. You don’t need to look further that the Haaros of R. Berel Levin on the bottom of the page to see how often he brings down a conflicting Minhag.
If you read the Sicha, as you said you have, you will know that the Rebbes Shita is that our Minhag cannot be in conflict with Halacha, ever. Therefore, the Rebbe does as much as he can to resolve this apparent conflict.