Most harnesses allow you to either tie into your belay loop or through the two loops the belay loop goes through. This does not really matter. The belay loop is tested with 15kN in the norm:
A load of 15kN is by far exceeding any load that could ever be applied. While the norm specifies a maximum of impact force of 12kN for single ropes, this is with a high fall factor, static belay and a metal mass instead of a human body. A more realistic maximum value for climbing is considerably lower.
The Petzl experiment also shows that the forces for the belayer do not increase when increasing the fall factor from 0.7 to 1, they are limited to about 2kN. At some point the belayer (if not anchored) is lifted off the ground and won't be able to apply more force on the belay end.
Looking at the numbers, we see that while the belay loop is a single piece failure, it is also considerably over-engineered in terms of load it can take. For belaying we are talking about a factor of 7-8
The real reason not to tie into the belay loop with the rope is that its more convenient when using double (half) ropes. If your climb is zig-zagging along a bit and you use one rope for the left side and one for the right side, it is very convenient to have these ropes left and right of your belay loop.