I think you should change the route via Tsuen Wan West Station, Tai Ho Road and Sha Tsui Road/Yeung Uk Road in at least one direction for the new 41M. Also, for the changes in 243M you can choose either changes but not both (e.g not stopping Cheung On - use my suggestion above; changing the route via Yeung Uk Road and Tsuen Wan West station, then you can go ahead with the new 41M.
Your second point is right.
However, many passengers travel on 41M from Tsing Yi to Yeung Uk Road and Tai Ho Road, and a number of them (near MTR station) cannot be served by 42M (via Yeung Uk road). Is there a solution of this?