The Nazi regime had planned to stage a big show trial for Thälmann, Elser and other enemies of their rule after a victorious end to the war. That is why they kept them alive. But by 1944 even the diehards knew that the war was lost. Hitler and Himmler gave orders to have Elser and others like Dietrich Bonhoeffer and Wilhelm Canaris killed. There was no time and no resources for such a trial at that late stage in the war.
A web site dedicated to the memory of Georg Elser shows a facsimile of the execution order for Elser. Dated 5 April 1945, the head of the Gestapo Heinrich Müller instructs the commandant of the Dachau concentration camp to have Elser discreetly executed and to announce his death from a "terror" (i.e., bombing) raid. Already in August 1944, they had disguised the murder of Ernst Thälmann as the casualty of an Allied bombing run.
There would have been no propaganda value from announcing Elser's summary execution after six years of imprisonment. And as mentioned, a planned show trial which was to have indicted the British as the instigators of Elser's failed assassination of Hitler was no longer feasible at that time. They were not going to allow Elser, Thälmann and other high-profile opponents to see the end of the war.
I have not been able to find any record of discussions among the Nazi leadership how their enemies should be disposed of and why they decided on the "cover story" of a bombing raid. Historian Peter Steinbach and political scientist Johannes Tuchel, probably the leading authorities on Elser and whose scholarship informs the above cited web site, do not touch on this point in their writings available online.
Two possible motivations appear plausible: one, the regime still clung to the facade of "law and order". Executions without a figleaf of legality would have undermined that facade. And two, some in the regime might have deluded themselves into thinking that they could escape facing responsibility for their crimes after the war if evidence of their worst deeds were covered up, especially if they were hoping for a negotiated capitulation and perhaps even some form of continuity for themselves in power.