Is it better to store the magnitude of an arbitrary-precision number in BigEndian or LittleEndian order in an integer array?
You are replacing magnitude[i] by magnitude[SZ-i]. That won't have any effect on complexity nor ease of implementation. Depending on the way simplifications occur, one or the other could have slightly less index adjustments, but I won't dare a guess which. Little endian seems slightly more in line with the usual presentations of the algorithms (for instance in TAOCP), big endian had a more intuitive representation of the number in memory, but that's an opinion more than a fact.

If you look at memory access patterns, there was a time when cache prefiller handled better increasing consecutive accesses (which would have favored little endian), but nowadays, I don't think it still make a difference at least on workstation and server processors.

So I don't think there is a compelling argument to choose BE over LE or ortherwise. Take the one which make you more at ease.