Ah, yes. This is the modern way of writing Sinhala. In modern Sinhala the binduwa (that circle) completely replaces the proper ṅa letter of ඞ. If you have a copy of one of the BJT books, you can see in the front that there is an alphabet chart. There you will see the “correct” way to write ṅa. But now the binduwa is used. However, that’s not a reason to start using the ṁ in transliteration.
But when that ṅ/ṁ sound comes before the semivowels, it is written with a binduwa, as in Saṁyutta: සංයුත්ත
[not quite related, but you will also notice that in literary Sinhala as used in the BJT there is not vowel remover (allkirima) and instead the letters touch each other. Those are the two big differences in traditional/literary Sinhala writing and modern.]
Yes, I don’t know why the manuscript here has it that way. If you use the “hover” dictionary you can see that there it is spelled saṅgha.
Here is the relevant part in the thread you linked to:
But to be clear, they are pronounced in the same way.