  The large temperature gradients in the solar transition region present a
significant challenge to large scale numerical modelling of the Sun's
atmosphere. In response, a variety of techniques have been developed which
modify the thermodynamics of the system. This sacrifices accuracy in the
transition region in favour of accurately tracking the coronal response to
heating events. Invariably, the modification leads to an artificial broadening
of the transition region. Meanwhile, many contemporary models of the solar
atmosphere rely on tracking energy flux from the lower atmosphere, through the
transition region and into the corona. In this article, we quantify how the
thermodynamic modifications affect the rate of energy injection into the
corona. We consider a series of one-dimensional models of atmospheric loops
with different numerical resolutions and treatments of the thermodynamics.
Then, using Alfv\'en waves as a proxy, we consider how energy injection rates
are modified in each case. We find that the thermodynamic treatment and the
numerical resolution significantly modify Alfv\'en travel times, the
eigenfrequencies and eigenmodes of the system, and the rate at which energy is
injected into the corona. Alarmingly, we find that the modification of the
energy flux is frequency dependent, meaning that it may be difficult to compare
the effects of different velocity drivers on coronal heating if they are
imposed below an under-resolved transition region, even if the sophisticated
thermodynamic adaptations are implemented.
