Dear Brian,
Sorry for the slow reply, I had a quick look at your example.
I think basically what you are seeing is a lack of convergence in the HEOM Matsubara decomposition (controlled by the N_k parameter) for the parameters you are using.
For example, T=10, and even T=100, are quite low temperatures when thinking about the bath cut-off and the system energies you are using, and its quite hard to get a converged result with the standard matsubara expansion.
The Pade decomposition is a bit better, but you still need to increase the N_k parameter quite a bit to see a reasonable result.
With the new environment class in qutip v5.1.0 (released a few weeks ago) its quite easy to plot the effective bath your system is seeing given a particular decomposition and cut-off N_k. I have updated your example to use this new interface, and use the Pade decomposition, and I think you should see more reasonable trends. If you dont want to update qutip you can probably still get a good result using DrudeLorentzPadeBath and a larger choice of N_k.
I also added a plot of the power_spectrum; essentially the one for the '''real bath'' and the one for the decomposition actually used by HEOM should look kinda similar. When the temperature is low there is a hard cut-off around zero frequency which the HEOM has trouble capturing, so you can see there is still some small error. In the new environment class
@Gerardo Suarez is adding a bunch of new fitting methods which might be useful for your case, but generally speaking it requires a bit of fiddling to get a good result out of these difficult regimes.
all the best
neill