If the 376s are just kept on the London Metro routes, then why is the lack of toilets any worse than London Underground, Overground and Liz Line trains? Or indeed the related 717 stock, which also doesn't have toilets?
The simple answer to this is that the South East London public has been used to having toilets on their trains since the Networkers came into service (i.e for over 30 years) thus not having them is (and was when the 376s were launched) seen as a step backwards. When the 376s launched there was an associated re-opening of station toilets in the metro area (only useful in staffed hours for smaller stations, not home-from-a-night-out urgent need to go times), and a statement that they would not go beyond Orpington or Dartford, which was very very short-lived. So whilst the general point stands, it's complicated by the local context of what is currently in place for the majority of services, and for the 376s the retrofitting of toilets on the 707s makes the lack of toilets stand out even more.
“More comfortable“ according to who? That’s never going to be an objective factor. The other points are.
The Networker seats are very comfortable - I seem to remember when Chiltern were refurbing their Turbos and ran a public consultation about the interiors the existing seats as also used on the Networkers due to their comfort. For me, and most people I've spoken to about this, which is more than you'd think, off peak you want in this order a 707 (air con, new and shiny, sockets) or a Networker (lots of seats, toilet), and a 376 gets a groan and an oh no (lack of seats, no air con/toilet/sockets, grubby). Peak times you may want a 376 over a Networker depending on where you are getting on because they are much better when standing is required due to the increase in space.