You're right that the placement in print of the sentence-ending period, following an expression that must be transcribed as spatial material, is inconvenient (to say the least).
I cannot point to a section in which either the Nemeth Code or the Guidance addresses sentence-ending punctuation and spatially arranged division. As you obviously know, sentence-ending punctuation that's followed by non-technical material belongs after the Nemeth Code terminator. So, I suspect that the most reader-friendly placement of the period you ask about would be immediately following the Nemeth Code terminator, even if that results in a braille line that contains nothing but a Nemeth Code terminator and a period.
Unrelated to punctuation: What if the word "Remainder" were uncontracted and treated as a label that's part of the synthetic division arrangement?
I hope that is helpful. Thank you again for the question.