Yes I agree I wouldn't have installed it anything like that and agree with you, always fit it right the first time dare than go back replacing the corners you have cut.
but just saying rip it out and start again is not a great help, and this fault is due to a different fault IMO.
He reality is no one really knows how well it's going to work once sorted, but when you are as balls deep as this now, it's worth trying to rectify before chucking the towel in completely. It's not the O.P's fault, whatever the price someone has been contracted to carry out this work. If they are confident they can get it running with this design then give them the benefit of the doubt.
if the O.P decides once/if it is running that it's not good enough, that is the time to question the design.
Whilst it's not our job to rectify, the post is asking for advice.
Its one of the more interesting posts anyway!