The assumption that something catastrophic happened in short time is not the only possibility. Probability for all chains of events leading to accident are low. One of those has sill happened and probable there are several things that had not gone right.
There was a hint that the plane might turn back. For me it sounds that they have consulted for problems and might have told that they will turn back if they can't solve the problems soon. For that reason the radio might have been in a “wrong” channel and the crew concentrated to “secondary” issues.
Then the situation might be turned rapidly from bad to worse and they have lost the transponder and some other systems. For mixed reasons they have found themselves in a situation where there is no time to establish communication and all the effort is needed to avoid the instant catastrophe. They also knows that the others can not detect them. So the diverted the region where is usually no traffic.
They also might have concluded that the emergency landing can be needed in a with a very short warning time if situation gets even worse. So they prepared to emergency landing by flying low. Then also the primary radars lost them, including military ones.
It could explain the confusion also in the ground. Primary radars detected the plane later but what a plane? They realized the detections only later when the plane was not found. At that time the “search train” was in the wrong rails and time has been lost.
Where the plane is? No idea. Lets hope not too far in the ocean.