Yemenite Hebrew has both [θ] and [ð] while a Greek sub-tradition has only [ð]. Would it make sense to use th for [θ] and dh for [ð] in the former case but th for [ð] in the latter (going by English orthography), or would it cause too much confusion when putting them next to each other? Would it make more sense to use dh for [ð] when discussing the Greek sub-tradition by itself?
How should I distinguish e.g. [sh] from [ʃ]? How should I maintain uniformity with traditions with no [ʃ] (e.g. some Lithuanians would pronounce שָׁנָתְהוּ [ʃonoshu] while others would say [sonoshu])? Is maintaining that uniformity necessary when putting the transliterations next to each other?