To answer this question, let's break the question down into smaller parts and analyse it piece by piece. First, we must understand what each of the reactions are.

An isodesmic reaction is a chemical reaction in which the type of chemical bonds that are broken in the reactant will be the same as the type of bonds that are formed as the reaction product. In thermochemistry, we normally associate this type of reaction as a hypothetical reaction.

Now let's look at the standard HOF, for many substances, the formation reaction may be considered as the sum of a number of simpler reactions. The enthalpy of reaction can then be analyzed using Hess's Law, which states that the sum of the enthalpy changes for a number of individual reaction steps equals the enthalpy change of the overall reaction. We know this is true as enthalpy is a state function.

Here's the important part. There are many different types of products formed during detonation. For instance, cobalt-60, cesium-137 and iridium-192. Immediately we can tell that none of these organic compounds. But let's say we're looking at the detonation of fuel in an engine's combustion chamber. The standard HOF cannot be measured directly as octane wouldn't break down into hydrogen and carbon. The reaction would now hypothetical due to the presence of organic compounds.

Now let's look at Atomization which refers to breaking bonds in some substance to obtain its constituent atoms in gas phase. Enthalpy of atomization is the amount of enthalpy change when a compound's bonds are broken and the component atoms are separated into individual atoms.

This is the key distinction between the two reactions. Where the isodesmic reactions always leave out the elements in standard state, this doesn't apply to atomization which accompanies the total separation of all atoms in a chemical substance.

For further reading that may arise from any misunderstanding of this query, listed below is a link to a reference paper that may help as well as add on any points missing from this answer.

Theoretical Studies on the Heats of Formation, Detonation Properties, and Pyrolysis Mechanisms of Energetic Cyclic Nitramines | The Journal of Physical Chemistry A (acs.org)

Hope this answer helps anyone who may have a similar question and do correct me if some of the points stated above are misconceptions.

The translation of energies to heats of formation via atomization and formation reaction procedures for molecules at 0 K successfully predicted within the G2 . Use of theoretical energies of the atomization reaction in conjuction with experimental data for the atoms may be associated with the fact that G2, G2(MP2), and G2 (MP2,SVP) .The energies have been optimized on the basis of atomization energies. Heats of formation for molecules at finite temperatures calculated via standard thermodynamic formulas

Heat of formation using isodesmic reaction and atomization reaction? when to use what?

in The systems G2, G2(MP2), and G2(MP2,SVP) total energies to heats of formation via atomization and formation reaction procedures is evaluated.

Both approaches give similar results, the former is shown to perform somewhat better, especially for organic molecules. The recommended general procedure for obtaining heats of formation at 0 K from G2-type total energies is to use G2-type atomization energies in conjunction with experimental gas-phase heats of formation for the constituent atoms. The corrections required to give heats of formation at finite temperatures can be obtained using scaled theoretically derived vibrational frequencies for the species under consideration together with temperature correction terms for the constituent elements based on experimental data. While the harmonic oscillator model is a good approximation for most vibrational modes, internal rotations with relatively low frequencies are more accurately treated within the free rotor approximation.