Looks like you can get SharedTable to respect references if your references are already SharedTables- Roblox skips over them, instead of making new copies.
Proof:
local SharedT = SharedTable.new({})
local T1 = {SharedT,SharedT}
local T2 = {SharedT,SharedT}
local X = SharedTable.new(T1)
local Y = SharedTable.new(T2)
print(X[1] == X[2])--> true
print(X[1] == Y[1])--> true