Context. The ongoing physical and chemical processes in planet-forming disks set the stage for planet (and comet) formation. The asymmetric disk around the young star Oph-IRS 48 has one of the most well-characterised chemical inventories, showing molecular emission from a wide variety of species at the dust trap: from simple molecules, such as CO, SO, SO2, and H2CO, to large complex organics, such as CH2OH, CH3OCHO, and CH3OCH3. One of the explanations for the asymmetric structure in the disk is dust trapping by a perturbation-induced vortex. Aims. We aimed to constrain the excitation properties of the molecular species SO2, CH3OH, and H2CO, for which we have used 13, 22, and 7 transitions of each species, respectively. We further characterised the extent of the molecular emission, which differs among molecules, through the determination of important physical and chemical timescales at the location of the dust trap. We also investigated whether the anticyclonic motion of the potential vortex influences the observable temperature structure of the gas. Methods. Through a pixel-by-pixel rotational diagram analysis, we created maps of the rotational temperatures and column densities of SO2 and CH3OH. To determine the temperature structure of H2CO, we have used line ratios of the various transitions in combination with non-local thermal equilibrium (LTE) RADEX calculations. The timescales for freeze-out, desorption, photodissociation, and turbulent mixing at the location of the dust trap were determined using an existing thermochemical model. Results. Our rotational diagram analysis yields temperatures of T = 54.8±1.4 K (SO2) and T = 125.5−3.5+3.7 K (CH3OH) at the emission peak positions of the respective lines. As the SO2 rotational diagram is well characterised and points towards thermalised emission, the emission must originate from a layer close to the midplane where the gas densities are high enough. The rotational diagram of CH3OH is, in contrast, dominated by scatter and subsequent non-LTE RADEX calculations suggest that both CH3OH and H2CO must be sub-thermally excited higher up in the disk (z/r ~ 0.17–0.25). For H2CO, the derived line ratios suggest temperatures in the range of T ~ 150-350 K. The SO2 temperature map hints at a potential radial temperature gradient, whereas that of CH3OH is nearly uniform and that of H2CO peaks in the central regions. We, however, do not find any hints of the vortex influencing the temperature structure across the dust trap. The longer turbulent mixing timescale, compared to that of photodissociation, does provide an explanation for the expected vertical emitting heights of the observed molecules. On the other hand, the short photodissociation timescales are able to explain the wider azimuthal molecular extent of SO2 compared to CH3OH. The short timescales are, however, not able to explain the wider azimtuhal extent of the H2CO emission. Instead, it can be explained by a secondary reservoir that is produced through the gas-phase formation routes, which are sustained by the photodissociation products of, for example, CH3OH and H2O. Conclusions. Based on our derived temperatures, we expect SO2 to originate from deep inside the disk, whereas CO comes from a higher layer and both CH3OH and H2CO emit from the highest emitting layer. The sub-thermal excitation of CH3OH and H2CO suggests that our derived (rotational) temperatures underestimate the kinetic temperature. Given the non-thermal excitation of important species, such as H2CO and CH3OH, it is important to use non-LTE approaches when characterising low-mass disks, such as that of IRS 48. Furthermore, for the H2CO emission to be optically thick, as expected from an earlier derived isotopic ratio, we suggest that the emission must originate from a small radial ‘sliver’ with a width of ~10 au, located at the inner edge of the dust trap.