Water boils at 100 degrees. Since it's likely not pure water, it will just boil slightly higher.
I think there is no need for a concern of whether it's freshly boiled or just hot water because it is not going to melt the plastic and most of these brands are bpa and bsa free.
Whichever water u are using, after u pour it to the container w the frozen breast milk in it, the temperature is only going to decrease. So everything is at 100 degrees and below - which is safe for most plastics - I think the concern is if u are boiling the bag of milk - which u are not doing.
Thawing in the fridge is recommended because it can be a longer process if thawed w hot water (require longer to melt and up the temperature)
The protein denaturation does not in anyway affect the nutritional value of the milk. People seldom use hot water as they scared to "overheat" to be too hot to be consumed immediately then u need to cool it down again - which can be time consuming especially if u have a crying hungry child. We eat denatured protein everyday - think boiled egg, or any cooked meat!
Btw, I do it too
Choon How Seow