Agree. Thought this was especially obvious last night, and was clearly something that Koeman had instructed them to do.
The other issue of course is that the system nullifies what was our single greatest attacking threat last season - Sane and Sterling running in behind the opponent's full-backs.
As you say, nothing wrong with having it as an option - though to be honest, I probably prefer last season's variation of the 3-2-4-1. Sure, it left us exposed to balls into the channel (thouh no more so than in the first 10 mins last night), but at least it meant that Sterling and Sane could play in their proper positions and we remained a real attacking threat. But in general, three at the back just doesn't really suit our current players and seems - to me at least - to be a system that, at the moment, detracts from, rather than maximises, our attacking potential. I find it all the more frustrating because a back four of Walker, Kompany, Otamendi/Stones and Mendy would be as good as anything in the league - I can't see what it is that Pep thinks the advantage of the extra centre half to be.