[MartinodF]

The rocket weighs quite a bit less at the end, having used most of its fuel, so only two engines are needed to land. The engines cannot be throttled down more than ~50% (as all rocket engines), so a third one would add too much thrust.

Falcon 9 does the same, relighting 3 engines (out of 9 total) for the boostback burn, 3 for the entry burn and then just 1 for landing.

[ygra]

For that flight the engines are even too powerful for the ascent (it wasn't fully fueled, I think) and as soon as they couldn't throttle any lower, an engine was turned off instead.

[Koiwai]

Thanks for the explanation! it this also the reason why Raptor is (relatively compared to like F-1) small and BFR uses so many of them?

[morlockabove]

That, and for redundancy. I've heard it's designed so that even if a significant number of engines malfunction, others can be used to compensate.