This ~3 km long section will remain as it is:
https://www.google.ch/maps/dir/46.93861 ... ?entry=ttu
I don't know if the new A4 is designed in a way to easily allow the filling of this gap, I hope so.
They choose to build two separate tunnels so as to build them in phases (the southern tunnel first, but I don't know if they finnaly have decided to build them together) and to operate them independently from each other, for instance during maintenance. I find the succession of separate tunnels more annoying than a single longer tunnel, but that's just my opinion. Also the gap is a pity, but that project is better than nothing and refusing it would mean doing nothing until 2080. Another gap is the roundabout near the junction of A2 and A4.
The first project had foreseen for a safety tube under the carriageway (that is, a space in the same tube separated by just a concrete floor, usable only by pedestrias, like in the San Bernardino and Mont Blanc), I don't know if they will still build them that way or if they will build a separate parallel tunnel. Separate tubes are usually big enough to be used by ambulances and small rescue vehicles.
Along the remaining gap there is one flat junction, which in addition is located in tunnel with limited visibility:
https://www.google.ch/maps/@46.9311397, ... ?entry=ttu