C64 always had basic built in. Because it was there you could assume it, and further it being there affected how the system booted. I'm was never a C64 guy so don't know what the options were for someone who didn't want basic.

The original Atari didn't have built in basic (the 2nd generation XL and your 3rd generation XE series both did). As such Atari programmers could never assume basic, and even when you could assume basic you couldn't assume the version, there were a few bugs in various versions. (I knew someone with a XL who used the earlier version of basic because the bugs in the XL version were serious enough to affect his usage).