I think Linus' comment is more on the lines of picking an endian-ness and sticking with it rather than having to check the specific stream and swap bytes condit

I think Linus' comment is more on the lines of picking an endian-ness and sticking with it rather than having to check the specific stream and swap bytes conditionally. He specifically mentions cases where the data is stored in BE and the program reads it, swaps it, operates with it, swaps it back again and writes it. The BE comment seems to me to be of much less importance than the other message (kind of like a side comment). And as you say, BE is very much alive today.